changes.txt

CHANGES BETWEEN 5.1.1 and 5.1.2 Official Releases

Bugs Fixed:
  - Supramap issue where dates in google earth are not normalized. (Thanks, Dan Janies)
  - Added 'nucleotides' for prealigned read-option (nucleotide was always present).
  - Removed arguments for clear_memory() command, they were unnecessary.
  - Fixed issues with OCaml 4.01.0+ where format strings were not being converted
    properly in our logging module.
  - Fixed issues with clang compilation
  - Removed function deprecations for newer versions of OCaml
  - Issue with trailing/leading spaces in CSV files for supramap (Thanks Dan Janies!)
  - Added support for OSX Yosemite (veclib -> Accelerate framework)
  - Fixed bug in sankoff distance calculation. The bug affects branch lengths and a
    heuristic on the cost of the tree, and not the actual cost.

Command Changes
  - removed transform(prealigned) (confusion with transform(ia)).
  - removed transform td, ti, trailing_insertion, trailing_deletion,
    auto_sequence_partition, auto_static_approx commands. These are internal to the system
    during the search. These commands had modified the ordering of results which is not
    appropriate for reporting the data.


CHANGES BETWEEN 5.1.0 and 5.1.1 Official Releases

Bugs Fixed:
  - Command swap(parallel) had issues with convergence and filtering trees.
  - Issues with gather after parallel search procedure in certain situations.

Known Issues:
  - We have experienced segmentation faults on POY compiled on OSX 10.9
    Mavericks with clang/LLVM3.3


CHANGES BETWEEN 5.0.0 and 5.1.0 Official Releases

New Features:
  - Script Analyzer has some resolutions for parallel analysis that should
    result in better performance of parallel execution.
  - swap(parallel) command, see below.
  - OPAM distribution via our github repo and basic_builder.sh. Please see our
    opam-amnh repo (http://github.com/amnh/opam-amnh)
  - Added initial level transformation of Aminoacid characters (during read);
    previously we reported this option was being ignored.

Bugs Fixed:
  - Reading morphology under Nexus had errors in processing SYMBOLS tag.
  - Reading Nexus files with single quoted taxa-names failed.
  - Parsering issue for trees with branch lengths in scientific notation and a
    plus sign in their exponent, 1.0e+09. Now accept '+' symbol. (Thanks Cyrille)
  - Under bremer (w/ negative constraints), nodes with excluded partitions were
    not properly scored (as infinity); this resulted in trees with lower score
    than expected during the bremer search.
  - Correctly implemented the prealigned amino-acid characters to accept
    resampling support techniques (jackkknife and bootstrap).
  - Minor issues with basic_builder.sh with install and ./configure with parmap
  - Certain level arguments were ignored since there are multiple ways to assign
    level arguments, through the cost matrix assignment, or as an additional
    argument (aminoacids and custom alphabet characters only).
  - Fixed inlining C functions to support CLANG / OSX Mavericks.

New Commands (see manual for full explanations):
  - Added documentation for commands in swap/build at_random, first, last. These
    control how trees of the same cost are selected in the search/build. The
    default is last, that is, the tree in memory is always replaced by the
    newest found during a search/swap/build/fuse.
  - swap(parallel) will swap in parallel a particular tree. This will allow
    large trees that require a lot of computation (dynamic likelihood) to be
    parallelized when a small number of trees are being analyzed. For example,

      ...
      build(1)
      transform(likelihood:(gtr,mpl,gap:coupled))
      swap(parallel,all)
      ...

    This will allow searching on the selected tree in parallel when the number
    of nodes in the MPI run is > 1. The 'all' option is recommended so that each
    node is fully utilized.

Known Issues :
  - We have experienced segmentation faults on POY compiled on OSX 10.9
    Mavericks with clang/LLVM3.3



CHANGES BETWEEN 5.0 beta2 and 5.0 Official Release

New Features:
    - Status messages for progress when using Model Selection and Fixed States
      transformation commands.
    - report(diagnosis) produces columns of only relevant information.
    - Improved error messages.
    - Updated Documentation.
    - Updated Test Suite and Tutorials.
    - New option for optimization level of dynamic likelihood (see below).

Bugs Fixed:
    - Script analysis would drop graphsupports command in finalized script.
    - Due to a number of issues when loading trees with taxa missing from the
      loaded data, we do not allow these trees to be loaded. The application
      will report the missing trees and skip loading the information. This can
      be used to generate a select command to filter terminals, like
        select(terminals, not files:("missing_terminals_file"))
    - General NonAdditive Characters causing error under Exhaustive DO. The
      appropriate functions not being called from previous testing.
    - Logic backwards in processing the level and orientation arguments for
      reading BreakInv and chromosome characters.
    - Loading data with unequal number of fragments (separated by #) did not
      cause an error, instead filled sections with "missing" data.
    - Issues with synonym files and processing trees (Ron Clouse)
    - Build under dynamic likelihood joined two nodes with different models.
    - Order of nexus blocks had Assumption block first, not last.

New Commands (see manual for full explanations) :
    - set( opt:exhaustive_dyn) will optimize the dynamic likelihood model
      directly, instead of via an implied alignment.



CHANGES BETWEEN 5.0 beta1 and 5.0 beta2

New Features:
    - report trees with branches would work for likelihood characters, but would
      not report parsimony branch lengths. The new command allows printing the
      branch lengths from three different methods (see below), these options are
      ignored under likelihood as we always report the parameter value that
      maximizes the log-likelihood.
    - report graphtrees, asciitrees, and trees with collapsible property have
      been extended to use the branch lengths mentioned above (see command
      description below).
    - Custom Alphabet transformation to static character via static approx. This
      was an issue with the characters that can be represented as prealigned and
      how to properly transform between them.
    - Added support for ocaml PARMAP for generating fixed-state cost matrices.
    - Added command report(robinson_foulds) (see command description below)

Bugs Fixed:
    - Selecting terminals caused an error in ncurses display when writing to an
      incorrect window (Louise Crowley).
    - Transforming to likelihood under a model selection criteria (aic,aicc,bic)
      from a tcm under parsimony with different gap cost than substitution cost 
      resulted (in failure) with added data that represents the cost of a gap.
      These should be filtered from the transformation, as in other likelihood
      transformations on those characters.
    - Custom-alphabet implied alignment produced an alignment with extra indels.
      This was due to an encoding issue that became relevant when mixing custom
      alphabet characters and levels.
    - Issue with missing data in custom-alphabet prealigned characters resolved.
    - generation of cost-matrix with all-elements row/col and non-zero diagonal
      cost matrix --was being replaced with zeros, should have been min of row.
    - No reported error when reading in sequence data with unequal fragments.
      This forced the computation to proceed as if those fragments were
      missing. Now (as in POY4) we report an error to the user.

New Commands (see manual for full explanations) :
    - report command for parsimony branch lengths
        report(trees:(branches:min))
            - minimum number of changes is reported on branches
        report(trees:(branches:max))
            - maximum number of changes is reported on branches
        report(trees:(branches:single))
            - number of changes reported based on single assignment of dynamic
              characters
    - report command for tree distances using Robinson Foulds distance metric
        report(robinson_foulds)
            - will print matrix to terminal window
        report("OUTFILE", robinson_foulds)
            - will print matrix to file OUTFILE

Changed Commands (see manual for full explanations) :
    - report command for collapsed branches has been changed. Instead of
      collapse:true or collapse:false, we've extended the command like the
      branch lengths above to collapse:min, collapse:max, collapse:single. The
      branch is collapsed when the length as defined above is equal to 0.0.
        report(trees:(collapse:single))
        report("tree.pdf", graphtrees:collapse:min)
        report( asciitrees:collapse:max )
 


CHANGES BETWEEN 5.0 alpha3 and 5.0 beta

New Features:
    - Consistency in alignment procedures across the application. The trace-back
      procedures produce the same result in affine (with gap opening equal to 0)
      as normal alignment procedures, as well as alignment procedures with speed
      increases (newkkonen), and the space saving algorithm.
    - Continuous characters are fully supported above the range of 0-255, now
      0 to the maximum size of integers on the machine. Although this change is
      slightly slower, characters that do fit in the 255 range are vectorized as
      previously implemented.
    - build(N,random) does not do a random Wagner build, but generates and
      diagnoses a random topology.
    - Sankoff and Sequence characters with matrices of non-0 diagonal elements
      have been implemented.
    - Information theoretic model selection procedures have been designed under
      static and dynamic likelihood (see new command below). This command can be
      used on multiple character sets and types of data in which case the model
      selected for each data-set are combined on the final tree(s). A tree must
      be in memory when the command is executed. The command analises all the
      models possible for each tree and selects the best based on the
      information criteria selected.
    - Updated build/compile procedures for different environments.
    - Implemented No Common Mechanism likelihood model (see new command below).
    - Bootstrap Probabilities under likelihood have been implemented. We use the
      same command as BP for other characters previously.
    - Better memory usage when loading multiple files of the same TCM.
    - Speed increases in the diagnosis of normal and affine sequence alignment.
    - Changed most (all found/possible) functions to tail-recursion to avoid
      stack-overflows, should also increase speeds.

Bugs Fixed:
    - Character Selection procedures (through the IDENTIFIERS in the command
      structure) have been verified and implement special cases of each-other
      when necessary for lower chances of future bugs. (Thanks to Fernando
      Marques).
    - Bug-fix with partitioned dynamic likelihood characters of multiple models
      or in combination with static characters causing optimization failures.
    - Error in transform(prealigned) on static characters --command only works
      on dynamic characters. These characters should have been ignored.
    - Likelihood model optimization routine returning matrix of NAN when branch
      lengths were sub-normal; minimum value has been used to avoid this.
    - Error in report(seq_stats) when missing data is present.
    - Proper usage of missing data in iterative:exact and iterative:approx.
      Previously missing data could be assigned in the median nodes of
      characters in certain situations, resulting in 0 costs assignments in
      subtrees, as well as errors in the median assignment functions. (Thanks to
      Denis Jacob Machado)
    - elikelihood for static likelihood characters had a bug in counting
      'uninformative' data in estimating transition probabilities.
    - Single assignment functions for the newkkonen alignment procedure were not
      calling the proper median function.
    - Static likelihood takes '?' into account correctly under fifth state (gap
      as an additional state) models. Previously it was interpreted as a gap,
      now it is interpreted as missing, like gaps in four-state models.
    - Static likelihood was not taking into account missing data correctly.
    - Correction for tree diagnosis in non-0 diagonal tcm matrix.
    - selecting unique topologies may choose suboptimal likelihood trees if the
      models/branches are different, we now select the lower of the two.
    - transform(likelihood(...) -> transform(parsimony) resulted in an error
      state of the application and incorrect costs from before the likelihood
      transform command. Now the transform can be done to recover the parsimony
      costs or vice versa.
    - Join caused a failure in fuse, causing failure in diagnosis of tree.

New Commands (see manual for full explanations) :
    - Command to set the optimization thoroughness for the likelihood procedures
      has been added. The command,
        set(opt:coarse)
        set(opt:exhaustive)
        set(opt:no_opt)
      determines the number of passes for the optimization algorithm, and the
      convergence factors for the numerical routines.
    - Information theoretic model selection for likelihood uses the same
      transform command as (e)likelihood, but replaces the model (ie. jc69, gtr)
      with an information theoretic criteria --aic, aicc, or bic. ie,
        transform(likelihood:(aic,rates:gamma:(4)))
    - No Common Mechanism (ncm) has been added as an additional model under
      likelihood. This is for static characters only. ie,
        transform(likelihood:(ncm))

Changed Commands (see manual for full explanations) :
    - reading prealigned characters (outside of nucleotides) have been unified
      with the normal command structure. For example,
        read( custom_alphabet:("DATAFILE", "MATRIXFILE"; init3D:true) )
      now is,
        read( prealigned:( custom_alphabet:("DATAFILE"), tcm:("MATRIXFILE")) )
      The previous command structure was only briefly implemented in an alpha.

Known Issues :
    - Pre-aligned affine data reports an incorrect cost. This option for
      analysis has been turned off and an error is reported.
    - Diagnosis on level over 5 creates a seg-fault. This is probably a memory
      issue as the function would exceed many computers limits.
    - Newkkonen space saving (set(space_saving_alignment)) command has been
      de-activated due to segfault.
    - 'help' commands generated from latex docs are a mess.



CHANGES BETWEEN 5.0 alpha2 and 5.0 alpha3

Bugx Fixed:
    - Continuous characters are fully supported from Hennig86/Nona files. The
      previous format that POY reads is the same (integers separated by spaces,
      missing data represented as '?', and ranges defined in square brackets
      separated by spaces. The data limit for the continuous characters requires
      a maximum range of 255. (Thanks to Edmundo Gonzalez)
    - Costs displayed on trees is incorrect for partitions/sets of characters.
      This is fixed to represent the overall tree cost.



CHANGES BETWEEN 5.0 alpha1 and 5.0 alpha2

New Features:
    - orientation set to true by default for breakinversion data-type.
    - faster alignment under low-mem settings

Bugs Fixed:
    - Fixed Makfile in src directory to perform the install, and removed the
      Makefile/configuration in the root directory. These files were synonyms
      for the ones the src directory and add no value to the compilation
      process.
    - Default for configuring with --enable-mpi is to set interface to flat.
      This is a requirement that is oft forgotten and there is no reason why we
      cannot facilitate that requirement. Setting interface to anything else
      will over-write that choice and report a warning.
    - Add Error message for input sequence with different number of
      fragments(fragments are devided by '#').  (bug report by Torsten Dikow).
    - Improved Makefile and Configure scripts from minor errors. Also removed
      Makefile and configure script from the root directory to avoid confusion
      and easier to maintain. (bug report by Jan De Laet).
    - Report lkmodel (to report likelihood model), was not working properly in
      certain situations; without identifiers.  (bug report by John Denton).
    - Transform likelihood with multiple types (for example a combination of
      static and dynamic) would fail in the transform due to alphabet size
      issues. We partition the data now between static and dynamic and then
      apply the transform to the characters. (bug report by Fernando Marques).
    - Used non-affine alignment for affine models under parsimony; this has
      been reverted correctly, and also includes affine low-mem ukkonen.
    - Compiling supramap and cmxs libraries dynamic linking rule was missing
      in our myocamlbuild file. (bug report by Travis Treseder).
    - Diagnosing Static and Dynamic Likelihood mixed models caused errors due to
      demarcation of sets of data. Resolved so we group by the type of model
      being applied to the characters as well as pre-defined sets and data
      classes.
    - Diagnosis for Dynamic Likelihood characters did not work on leaf nodes.
    - Backtrace works the same in POY4 and POY5 for normal alignment; the issue
      is in regard to the preference in inserting indels in which sequence.
    - Affine alignment bug with aligning two sequences at a point each having 
      gap polymorphisms. This is a very rare instance.

New Commands:
    - set(space_saving_alignment)
    - set(normal_alignment)
        - commands turn on/off low-memory alignment procedure. Default off.

Changed Commands:
    - transform(chromosome:(newkkonen,..)
    - transform(genome:(newkkonen,... ))
        - this option is specified in the low-memory/space-saving alignment
          procedure mentioned above.



CHANGES BETWEEN 4.1.2.1 and 5.0 alpha1

New Features
    - Added likelihood criterion for diagnosing trees.
        - Added methods of optimization for likelihood during build/swap/fuse
        - Support for dynamic and static characters under a variety of models.
        - Most Parsimonious and Maximum Average Likelihood cost models.
        - Static and Dynamic character support for likelihood, including any
          alphabet size (ie, discrete morphological characters, amino acid, ...)
    - Added a variety of median solvers for rearrangements.
    - Support for Genome and Chromosome characters with annotator Mauve.
    - New selection method for polymorphic data in fixed state characters.
    - Added level support on all alphabets sizes.
    - Changed default TCM to 1,1.
    - Updated configure scripts for newer versions of gcc and ocaml.
    - Low memory option for alignment of sequences.
    - Changed command for transform for dealing with identifiers.
    - Require one type of delimiters in data files.
    - Choice of equally costly medians can be user specified.
    - pre-aligned for custom-alphabet and amino-acid characters.
    - Allow additional medians by search-based command for fixed state
      characters.
    - Internal assignment in diagnosis output of fixed state characters print
      taxon name.
    - Default for amino-acid to not use 3D alignment in up-pass
    - Better support for manipulating and calling character sets in data
    - Graphic output for mauve outlining alignment of blocks and rearrangements

Bugs Fixed:
    - Memory leaks in grappa interface.
    - Building random trees does not use a modified Wagner build.
    - Missing data is presented as a '?' in output from implied alignments.
    - Avoid rediagnosing trees before certain operations.
    - Issues in reading prealigned phylip files.
    - Better support for all features of NEXUS files.
        - Added POY block to nexus files for our specific needs, including
          likelihood, chromosome, genome, and dynamic character information.
    - Detecting file types is more accurate.
    - Parsing file types has better support.
    - Can transform Break Inversion and Custom alphabet with cost matrix file.
    - Replaced command dynamic_pam to deal with new datatypes.
        - now chromosome, genome, breakinv, etc.
    - Priority for backtrace in the alignments standardized between floating
      point alignment (dynamic likelihood), affine, and sequence characters.
    - Nexus output is fully produced when called in the report command
      --includes trees, set information, data, etc.
    - Support for scientific notation of floating point numbers in parsers.
    - Custom Alphabet and Break Inversion data characters case sensitive.
    - Fixed and improved POY help documentation 
    - Initial cost for downpass in fixed state characters was incorrect (up-pass
      and final costs were correct).
    - Status messages during branch and bound build (after every 1% complete).
    - 3D option set to false is observed after re-diagnosis.
    - all element code (X) in amino acid is treated as a polymorphism
    - Improved max_time behavior in searching
    - Fixed cost issue in rearrangement for annotated characters

Features eliminated:
    - dynamic_pam command has been replaced by the commands chromosome, genome,
      breakinv, and custom_alphabet.

New Commands:
    - transform( likelihood:( ... ) )
    - transform( genome:( ... ) )
    - transform( chromosome:( ... ) )
    - transform( breakinv:( ... ) )
    - transform( custom_alphabet:( ... ) )
    - transform( parsimony )
    - transform( level:INT )
    - set( partition:( ... ))
    - set( codon_partition:( ... ))
    - swap/fuse/build( optimize:(model:(...),branches:(...)) )
    - report( trees:(branches) )
    - report( lkmodel )

Changed Commands:
    - transform( [IDS], (transformations,...) )
    - read( custom_alphabet:([datafile],[costmatrix],[prealigned]))



CHANGES BETWEEN 4.1.2 and 4.1.2.1

New Features:
    - Added support for NEXUS output in the portal binary.

Bugs Fixed:
    - Output of NEXUS files when terminals are filtered, 
      or dynamic homology characters are not present could 
      produce errors or a file that POY itself could not 
      read (Felipe G. Grazziotin).



CHANGES BETWEEN 4.1.1. and 4.1.2

New Features:
    - Added build (nj) to build a tree using the neighbor joining
      algorithm. The algorithm implementation is deterministic, so
      only one tree can be produce for each dataset.
    - Added read (prealigned:(....., gap_opening:INT)) to read
      prealigned sequences and assign each indel block a gap opening
      cost.
    - The build process now uses ocamlbuild instead of plain
      Makefiles. 
    - The distributed binaries are the first to support plugins for
      POY, but the feature is still experimental.
    - Improved the NEXUS file format support, by adding the POY block,
      which now includes: GAPOPENING, TCM, and WTSET. All the
      characters in POY can now be stored in one NEXUS file that can
      be reloaded later. The support for NEXUS files has improved to
      allow more transparent interaction with other applications.
    - POY now interprets all the ASSUMPTION block commands in NEXUS
      files that the program can apply (e.g. EXSET, TYPESET, and
      USERTYPE).
    - Added report (nexus) and report (trees:(nexus)) to generate
      output in nexus format. 
    - report ("out.ext", data, trees) produce NEXUS or hennig format
      depending on ext. If the extension of the filename to which data
      and trees are generated is "nexus" or "nex" then the data and
      trees are generated in NEXUS format. If the extension is "hen",
      "hennig", or "ss", then the format is Hennig86. For example,
      report ("out.nexus", data,trees) is equivalent to report
      ("out.nexus", nexus, trees:(nexus)).
    - Replace spaces with underscores in taxon names of NEXUS files.
    - Added support to newick files with branch lengths. The branches
      are ignored.
    - Added support to 1~4 ranges.
    - Bremer support values can output on the branches of a consensus
      tree or any user provided input tree. (See the new commands
      below.)

New Commands:
    - report (nexus trees:(nexus)).
    - transform (dynamic_pam:(locus:dcj:INT))
    - report (supports:bremer:of_file:("file1", "file2", ...)) 

Features eliminated:
    - Dropped ti and td
    - ':' is not accepted in a taxon name, required for newick file
      format. For example "mytaxon:1" is not an acceptable taxon name
      anymore.

Bugs Fixed:
    - Fixed issue 72.
    - Fixed incorrect description of select (missing) in the
      documentation.
    - Annotated chromosomes could produce incorrect costs 
    - Fixed compilation problems of the portal
    - Data.get_tcm2d error (Buz Wilson, Katrina Menard).
    - Sankoff characters where not applied the user defined weight.
    - Branch collapsing in Sankoff and Additive characters could be
      incorrect.
    - Tree scores with additive characters may be incorrect (Taran
      Grant). This only happened if the additive character had state
      7.
    - search (constraint) and swap (constraint) have multiple fixes to 
      better guarantee the restrictions set by the constraint.
    - 0 length branches now appear with 0 bremer support when bremer is 
      reported.
    - Fixed compilation error in Mac OS X 64 bits using OCaml 3.11.0.
    - The total rearrangement cost included indels for rearranged
      elements.



CHANGES BETWEEN 4.1 and 4.1.1

Improvements:

    - Simplified naming of single fragments and partitioned sequences:
      now the number only appears if more than one fragment is loaded.
      For example, if a file a.fas has only one fragment, the old
      naming convention for that character was a.fas:0.  The name for
      the character is now a.fas.

    - Improved the message for bad NEXUS files comming from Mesquite.

Bugs Fixed:

    - search () used too much memory in some cost regimes, causing a
      dramatic drop in the application performance when searching
      those costs.



CHANGES BETWEEN 4.0.2911 AND 4.1

Improvements:
    - Improved detection of inconsistencies in synonym files.
    - ci and ri could fail with a Not_found error when static 
      homology characters where missing in an input file.
    - The characters produced from an implied alignment keep
      the name of the original sequence character. For example, 
      the first base in the implied alignment of chel.aln:0 gets
      the name chel.aln:0:ia:0.
    - Improved the graphical output, now in pdf format.
    - If the synonyms file is not found, POY stops the script
      execution.
    - New command to report bremer values using multiple input files
      containing trees collected during a search.  For example, if a
      user has 5 separate files containing trees collected
      independently using swap (visited:"file1"), swap
      (visited:"file2")..., swap (visited:"file5"), then the created
      files can be used to produce the bremer support values using
      report (supports:bremer:("file1", "file2", ..., "file5"))
    - New command report (supports:[jackknife|bootstrap]:"FILE") and
      report (graphsupports:[jackknife|bootstrap]:"FILE"). FILE
      contains input trees, and the report contains those trees with
      the corresponding support annotations. 
    - Added support for compression using the zlib library in bremer
      files using swap (visited:"file"). The files produced can be
      decompressed with gunzip.
    - Removed the need to make depend before compiling any target.

Bugs Fixed:
    - swap with non-additive characters can fail with segfault.
    - swap (visited:"file") fails in windows.
    - Diagnosis of Sankoff characters could fail.
    - Sankoff characters diagnosis in XML did not print correct human
      symbols.
    - Bogus warning message when reading a list of trees.
    - Compressed bremer files fail to use all of the trees.
    - Additive characters do not appear in the diagnosis.
    - Improved the precission of the maximum time when using search ()
    - Fixed stack overflow / seg fault when reading a large number of
      trees.

New Compilation Requirements:
    - Made OCaml 3.10.2 or superior a requirement (due to Camlp4
      bugs).
    - POY now needs the zlib library.



CHANGES BETWEEN 2885 AND 2911
    BUGS FIXED:
    - Printing long trees in parenthetical notation could cause a crash.
    - After compiling with --enable-xslt poy behaves as if not enabled.
    - Transform (static_approx) with aa characters can fail.
    - Test build/build9.poy fails.
    - Issue#69 and some improvements to the Makefile rules.
    - Multiple improvements and bugfixes in the swapers and tabu managers.
    - Compressed files did not handle \r\n -> \n conversion in win32.
    - Crash in Mac OS X - PPC.
    - Fixed bug in the phastwinclad output.
    - Hennig and Nexus parsers do not handle polymorphisms.
    - Issue #67
    - Iterative pass under affine and missing data could assing power sequences
      (and therefore incorrect tree cost).
    - Reading some very large files could cause a stack overflow error.
    - Some input file channels where never closed, and many forks can be used.
    - Windows fails on report (supports:bremer:"x") 
    - read (prealigned:("x", y)) some times fails.
    - reading trees containing synonyms after rename () does not work.
    - report (supports:bremer:"file") contained values for the root.

    IMPROVEMENTS:
    - Significant improvements in the performance of search (): it finds
      better trees.
    - Added -enable-xslt to the top configure for help purposes.
    - Added support to make install DESTDIR=path
    - Upon reading trees, POY verifies that all the loaded terminals are
      present.
    - Some times WinClada fails to read trees in Hennig format.
    - Reduced memory consumption in XML conversion functions.
    - Changed from Error to Warning the "You are loading a non-metric TCM"
      message.
    - Added XML file for SWAMI bioinformatics portals, and the companion
      poy_server program.



CHANGES BETWEEN 2880 AND 2885:
    - Bugfix: Reading some very large files could cause a stack
      overflow error.
    - swap (visited:"f") and report (supports:bremer:"f") compress the
      file f.
    - Bugfix: swap (visited) could print the wrong cost when only
      static homology characters have been loaded (Taran Grant).
    - New Arguments: report->searchstats, build->threshold,
      build->lookahead, transform->max_kept_wag
    - Improved the handling of the program arguments for better
      execution in more implementations of MPI.
    - Bugfix: Static approx fail to add gaps in non-affine sankoff
      matrices.
    - Bugfix: Make sure that characters that should be ignored
      according to the Nexus and Hennig files are indeed ignored.
    - Bugfix: help () did not work! Issue# 65.
    - Multiple documentation improvements.
    - Bugfix: Missing sequences could cause bogus 0-length branches in
      the tree.
    - Improved build (_mst).
    - Bugfix: Duplicate character names in input files overwrite older
      ones.
    - Bugfix: Hennig/TNT parser do not accept empty comment in xread
      command.
    - Bugfix: The ncurses interface some times, misteriously,
      internally deletes characters that are not deleted in the
      screen, producing illegal commands.
    - Improved error messages for Mesquite's TITLE command in NEXUS
      files.
    - Improved detection of Hennig/NONA/TNT files.
    - Eliminated the full help on command errors. This is only
      confusing.
    - Improved the behavior of the GenBank file format parser.
    - Bugfix: Equate within polymorphisms didn't parse in
      Hennig/Nexus.
    - Hennig parser now interprets the nstates command.

CHANGES BETWEEN 2870 AND 2880:
    - Improved static approx for annotated chromosomes.
    - Fixed multiple bugs in the implied alignment for chromosomal and genome characters
    - Issue #55: Sorted the characters by code in report(crossreferences:names:("x")).
    - Issue #57: Use non-additive characters in more cases after static approx.
    - Fixed typo in report (memory) (Campations is Compactions).
    - Issue #58: read ("unexistant") causes a hang in POY when running in parallel.
    - Fixed bug in genome alignment
    - Documentation update: Reference filed partially updated to reflect more uniform 2 intial format.
    - Fixed Issue #56 and added set (iterative:false).
    - Cleaned some harsh words in source code.
    - Fixed cost matrix problem in the genome character
    - Improved various details in the set (iterative:false) algorithm.
    - Fixed Issue# 59 and removed bogus user messages.
    - Added the options iterative:exact and iterative:approximate.
    - Fixed Issue #60
    - Modified heuristic of search (), and fixed diagnosis bug under iterative.
    - Fix a bug in suffix tree creation.
    - Bugfix: transform (weight) does not automatically update trees in memory.
    - Improved the behavior of the tree selection under negative weights.
    - Bugfix: accept negative values for random number generator seed.
    - Minor fixes in report(data)
    - Added seq.h header to eliminate a compile time warning.
    - Added files to ignore from the documentation and compilation accessory files.
    - Bugfix: Issue #61
    - Bugfix: help (search) shows many results but not just the command search.
    - Bugfix: help (search) shows a paragraph with vertical boxing (missing brackets).
    - Bugfix: help (search) shows all the See Also items in one line.
    - Added man pages.
    - Bugfix: Issue #62
    - Bugfix: The Fixed States field of report (data) is always empty.
    - Handle negative segments in chromosomes when creating implied alignment
    - Take into account inverted segments in annotated chromosomes
    - Bugfix: Fixed a wrong case handling in the diagonal extension opening a gap.
    - Simplified the execution of the changes introduced in the previous commit.
    - The iterative algorithm now follows a postorder traversal.
    - Added search->visited argument.
    - Added search->constraint
    - Fixed bug in file constraint ignored during break.
    - Change kept_wag default value from 3 to 2
    - Activated iterative algorithms for chromosome characters
    - Improved 3D-chromosome and genome alignments
    - Fixed bug in build with internal transform.
    - Fixed bug in analyzer for expressions like build (10, transform (static_approx))



CHANGES BETWEEN 2635 AND 2870:

Improvements:

    - Added a new initial assignment of sequences using fixed states.
    - Added the new argument transform -> direct_optimization and
      modified transform -> fixed_states.
    - Multiple crashes in parallel execution have been corrected.
    - Massive improvements in affine gap cost.
    - Added filters for redundant tree evaluations during spr and tbr.
    - Improved TBR.
    - Changed the default swap strategy from alternate to TBR.
    - Improved the command search ().
    - Newick is the new default format for all the parenthetical tree
      output functions.
    - Reduced memory consumption by more than half for DH chars.
    - Improvements in the performance of perturb operations.
    - Added the command set->timer:INT.
    - Limited number of rediagnosis performed during search.
    - Improved the performance of swap(constraint).
    - Disabled iterative in non-sequence chars.
    - Modified the following arguments for better readability:
        1. seq_to_breakinv -> custom_to_breakinv
        2. breakinv_to_seq -> breakinv_to_custom
        3. breakpoint -> locus_breakpoint
        4. inversion -> locus_inversion
        5. approx -> med_approx
        6. sig_block_len -> min_loci_len
        7. rearranged_len -> min_rearrangement_len
    - Speedup tree fusing.
    - Modified timeout's behavior (see documentation.)
    - Moved the select (terminals) report from stdout to stderr, where
      it belongs.
    - Improved transform (static_approx) when using affine and sankoff
      tcm's.
    - Simplified representation of SankCS.t to reduce memory
      consumption.
    - Reduced the number of reports of the current search state.
    - Improved tree fusing by not swapping those trees that are
      already in the population.

Compilation Changes:
    - New Configure Option: --enable-large-messages. See ./configure --help.

Bugs Fixed:

    Bugfix:
        Symptom:
            Searches under gap_opening:x can fail with a segmentation 
            fault (Buz Wilson).
        Problem:
            The computation of the medians under affine is not atomic, 
            yet some heuristics assumed they where, breaking some 
            invariants.
        Solution:
            Store the complete median for use, and don't recompute the 
            individual medians.

    Bugfix:
        Symptom:
            Certain scripts containing wipe () fail to be analyzed 
            (Lara Lopardo).
        Problem:
            The analyzer has a glitch for wipe () and use ().
        Solution:
            Analyze the portions separation by wipe () and use () 
            independently.

    Bugfix:
        Symptom:
            Orientation and init3D are true even if the user doesn't
            set it to that value.
        Problem:
            We check if the list of options does not contain 
            `Orientation false or `Init3D false, but the default 
            selection contains an empty list, makeing this true.
        Solution:
            Check if the list of options contains `Orientation true 
            or `Init3D true.

    Bugfix:
        Symptom:
            Reading an input tree when data some terminals have been
            selected causes a Not_found error.
        Problem:
            We assign code in the tree by counting the number of
            leaves instead of the number of taxa loaded in Data.d. 
        Solution:
            Use the parameter in Data.d.

    Bugfix:
        Symptom:
            transform (randomize_terminals) fails with a Not_found
            error.

        Problem:
            We eliminate all the data and recompute the tree de novo.
            But before recomputing we compare the nodes to see if
            something really needs to be recomputed, the problem is
            that some of the nodes are missing!

        Solution:
            force the update and if the error occurs, trigger the
            update.

    Bugfix:
        Symptom:
            report (diagnosis) may show some bogus character states.
        Problem:
            The reported characters remain classified in groups,
            therefore, for some of the input characters, the reported
            states may not match, thought the overall cost is correct.
        Solution:
            Reload the tree with the raw nodes, without
            classification.


    Bugfix:
        Symptom:
            transform () together with use () and store () may result
            in empty datasets.
        Problem:
            The nodes are not necessarily regenerated when the data is
            loaded back with the use () command. 
        Solution:
            To avoid this problem, we store both the data and the
            nodes, and use them when requested. This has 0 speed
            penalty, and some memory penalty.
        
    Bugfix:
        Symptom:
            If there are 0 characters loaded, a Random.int error is
            raised when the calculate_support (bootstrap) command is
            issued.
        Problem:
            We don't verify if the number of characters is greater
            than 0 before doing the resample, and Random.int requires
            a positive integer.
        Solution:
            If there are 0 characters, there is nothing to resample.
            Just return the same array.

    Bugfix:
        Symptom:
            Assertion failure when the input tree contains terminals
            that don't exist in the input files.
        Problem:
            We don't verify the leaves before attempting to build the
            tree, which has now a predefined set of codes. If the
            input tree contains _more_ leaves than vertices require
            the input data to produce a tree, the program will break
            an assertion.
        Solution:
            Check the leaf names before attempting to load the tree.

    Bugfix:
        Symptom:
            read ("bleh") produces a background File Not Found
            messages in windows, which can appear anywhere in the
            screen.
        Problem:
            We don't use proper handling of stderr in the windows port
            for this kind of command.
        Solution:
            Redirect stdin, stderr, and stdout, ignoring the first two
            completely in every architecture, by using not the system,
            but directly OCaml's Unix module.

    Bugfix:
        Symptom:
            Some times POY prints a large number instead of INF for
            trivial Bremer support values.
        Problem:
            We check if the number is large, but floating point
            comparison may fail.
        Solution:
            We now do a rough comparison for a number half of the
            internal infinity number (Pervasives.float_of_int
            (Pervasives.max_int / 4)) and if larger, then we assume it
            is just infinity.

    Fixed typo in Perturbing message (was Perburbing) (Buz Wilson).

    Bugfix:
        Symptom:
            Reading a nexus file with comments inside the matrix
            itself failed with Segmentation fault.

        Problem:
            We have an endless loop that causes an Stack Overflow
            error, which can be a segmentation fault in some
            architectures.

        Solution:
            Fix the endless loop by incrementing the counter before
            making the recursive call.

    Bugfix:
        Symptom:
            Reading UNALIGNED blocks in NEXUS files fails.
        Problem:
            Internally we convert the NEXUS matrix into a FASTA file,
            but the generated file is ... incorrect.
        Solution:
            Make sure that the resulting file is correct.
            
    Symptom: 
        read (aminoacids:("A")) transform (tcm:(1,1)) report (ia)
        fails with a Not_found error (Boyan Alexandrov).
    Problem:
        The gap code is not the last code of the alphabet, which is an
        assumption of the tcm generator.
    Solution:
        Exchange the integer code of the X and the gap.

    Symptom:
        Tree fusing fails when running static homology characters only
        (Ward Wheeler).
    Problem:
        When using static homology characters only, no information is
        attached to an edge, but the functions assume (and assert)
        that there is indeed information associated with an edge.
    Solution:
        Generalize the code to consider the other possible set of
        algorithms.
    
    Fixed bug in the serialization of the three dimensional cost
    matrices.

    Symptom:
        During parallel execution, if the dataset includes additive
        characters, POY may crash (Fernando Marques).
    Problem:
        The serialization functions for additive characters did not
        use proepr macros for 64 bit and 32 bit environments. They
        also assumed that successive mem_malloc calls would produce
        successive memory locations (clearly incorrect).
    Solution:
        Define the required macros to handle properly native integers,
        and serialize and deserialize all the vectors independently.

    Symptom: 
        poy script.txt when poy is compiled in parallel fails for the
        following script:
            read ("x")
            build (10)
            select ()
            swap ()
            report (trees)
        with the Warning: "No trees in memory" (Fernando Marquez)
    Problem:
        The `GatherTrees command does not run the merging instructions
        if only one process is being executed.
    Solution:
        For every branch of the tree exchange algorithm, run the
        joiner set of instructions.

    Symptom: 
        Issue 51 (loucrow and Fernando Marquez).
    Problem:
        The GatherTrees command had some bugs in the way it was
        merging trees from different processes. 
    Solution:   
        Simply merge the stored_trees and trees fields from
        Scripting.run and do not postprocess trees thanks to the
        change described above.

    Symptom:
        Reading a NONA/TNT file produces trees rooted in the last
        terminal of the file (Federico Lopez).
    Problem:
        The parser of NONA/TNT files, just as the Nexus parser,
        produces the output in inverse order.
    Solution:
        Repeat the solution for Nexus files in 2635 with NONA/TNT
        files.
    
    Symptom: 
        select (terminals, "filename") outputs a table of included and
        excluded for each slave.
    Problem:
        Although we filter output for slaves, table output is not
        being filtered out.
    Solution:
        Filter the table output to include only output requests from
        the slaves.



CHANGES BETWEEN 2602 AND 2635:

Bugfixes:
    - read (prealigned:("file.txt", tcm:(1,1))) report (phastwinclad)
      prints an error when file.txt contains fragments and some
      fragments are missing (Julian Faivovich).

    - Removed a bogus @ sign in the description of an input file type.
    
    - An error appears for chromosome characters when iterative pass
      is set before swap command.

    - ./configure --enable-interface=readline; make fails under x86-64
      linux (Dan Janies)

    - The first taxon in a nexus file is treated as the last one
      instead of honoring the input file order. This makes the last
      terminal the effective default root for nexus files (Federico
      Lopez).

    - Fixed Issue #49
    - Fixed Issue #48
    - Fixed Issue #45 
    - Fixed Issue #40
    - Fixed-Partial Issue #38
    - Fixed Issue #37
    - Fixed Issue #20

Improvements:

    - subversion is not required to compile anymore and versions
      compiled using the code.google.com site as well as the
      downloaded source code have the correct build number.

    - Added message to the Search Status showing the current tree cost
      calculation algorithm.

    - Made the selection of a root of a tree deterministic (for cost
      calculations).

    - Reduced the number of tree diagnosis during OnEachTree
      operations and after reading an input file. This should reduce
      considerably the execution time for non-trivial tree sizes.



CHANGES BETWEEN 2398 AND 2602:
------------------------------------------------------------------------
r2588 | andres | 2008-02-04 17:23:35 -0500 (Mon, 04 Feb 2008) | 8 lines

Bugfix:
    Symptom: 
        Issue #36
    Problem: 
        A newline is hinted to the pretty printer, but it is almost never used.
    Solution:
        Make the newline an obligatory one.

------------------------------------------------------------------------
r2587 | andres | 2008-02-04 14:24:53 -0500 (Mon, 04 Feb 2008) | 3 lines

Improvements: Hardcoded the machine that takes care of the generation of the
release binaries.

------------------------------------------------------------------------
r2586 | andres | 2008-02-04 14:23:57 -0500 (Mon, 04 Feb 2008) | 15 lines

Bugfix:
    Symptom: 
        Running POY in parallel produces duplicated output for many functions.
        Running POY in parallel in windows produces an MPI error message at the
        end.
    Problem:
        We use the rank of the process to decide how to do IO. Only process 0
        (the master), is allowed to produce output, otherwise it should be piped
        through the master as plain messages. This is not being done properly in
        the html interface which is used in the GUI based parallel execution.

    Solution:
        Make a uniform interface and set the rank when the parallel printer is
        set upon the program initialization (Status.is_parallel).

------------------------------------------------------------------------
r2585 | andres | 2008-02-02 18:44:13 -0500 (Sat, 02 Feb 2008) | 4 lines

Bugfix:
    A bogus test failure due to an incorrect cost stored in one of the test
    files.

------------------------------------------------------------------------
r2584 | andres | 2008-02-02 10:45:36 -0500 (Sat, 02 Feb 2008) | 5 lines

Improvements:
    Automatically cleanup the temporary files (to reduce the ammount of garbage
    left after a test), and if not needed, leave the output going directly to
    stdio so that the buildbot catches the results.

------------------------------------------------------------------------
r2583 | andres | 2008-02-01 18:19:19 -0500 (Fri, 01 Feb 2008) | 4 lines

Bugfix:
    Modified the test_line program to properly signal buildbot when there is an
    error in a batch of tests.

------------------------------------------------------------------------
r2582 | andres | 2008-02-01 17:02:19 -0500 (Fri, 01 Feb 2008) | 3 lines

Improvements:
    Added compilation rules for poy_test at the top level.

------------------------------------------------------------------------
r2580 | andres | 2008-02-01 14:15:29 -0500 (Fri, 01 Feb 2008) | 4 lines

Improvements:
    Added the new ocaml-flags options from the src/configure.ac to the topmost
    configure file.

------------------------------------------------------------------------
r2579 | andres | 2008-02-01 14:15:05 -0500 (Fri, 01 Feb 2008) | 4 lines

Improvements:
    Multiple improvements in the randomTree utility. See the --help for more
    information about the new options and their behavior.

------------------------------------------------------------------------
r2578 | andres | 2008-02-01 13:30:09 -0500 (Fri, 01 Feb 2008) | 7 lines

Bugfix:
    Symptom: Compiling with the html interface fails.

    Problem: There is no Warning constructor in Status_html

    Solution: Add the constructor.

------------------------------------------------------------------------
r2575 | vinh | 2008-01-30 08:36:23 -0500 (Wed, 30 Jan 2008) | 2 lines

Continue working on iterative pass for chromosome characters

------------------------------------------------------------------------
r2574 | andres | 2008-01-25 18:11:50 -0500 (Fri, 25 Jan 2008) | 5 lines

Improvements:

    Added the constructor Status.Warning for warning messages. This resolves
    Issue #24 in a clean manner.

------------------------------------------------------------------------
r2573 | andres | 2008-01-25 17:57:41 -0500 (Fri, 25 Jan 2008) | 6 lines

Bugfix:
    Symptom: Issue #33
    Problem: We don't add the files whose type is not autodetected to the list
    of read files.
    Solution: Add all the files whose type is specified by the user.

------------------------------------------------------------------------
r2572 | andres | 2008-01-25 17:46:33 -0500 (Fri, 25 Jan 2008) | 4 lines

Bugfix:
    Symptom: Issue #34
    Problem: We never handled these cases in the script postprocessing.

------------------------------------------------------------------------
r2571 | andres | 2008-01-25 10:09:56 -0500 (Fri, 25 Jan 2008) | 12 lines

Bugfix:
    Symptom: 
        running tests with only one processor doesn't generate test_all.log
        (Megan Harrison)
    Problem: 
        The script uses Unix.waitpid () although tests with only
        one processor have no children processes. This causes a
        non-handled exception, skipping the necessary file concatenation
        functions.
    Solution:
        If only 1 process is requested, skip the Unix.waitpid function.

------------------------------------------------------------------------
r2570 | andres | 2008-01-23 11:32:34 -0500 (Wed, 23 Jan 2008) | 4 lines

Improvements:
    Added options for the selective compilation of windows binaries. Check bash
    win32_build.sh --help for more information.

------------------------------------------------------------------------
r2569 | andres | 2008-01-23 11:05:32 -0500 (Wed, 23 Jan 2008) | 3 lines

Improvements:
    Cleaned up the parallel execution message added in 2568.

------------------------------------------------------------------------
r2568 | andres | 2008-01-23 10:50:29 -0500 (Wed, 23 Jan 2008) | 4 lines

Improvements:
    When executing in parallel, the initialization messages report the number of
    processes being executed.

------------------------------------------------------------------------
r2567 | andres | 2008-01-23 09:56:15 -0500 (Wed, 23 Jan 2008) | 4 lines

Improvements:
    Reduced the verbosity of the program by turning off the node loading status
    messages.

------------------------------------------------------------------------
r2566 | andres | 2008-01-18 11:32:33 -0500 (Fri, 18 Jan 2008) | 2 lines

Removed the debugging flag which was committed by mistake.

------------------------------------------------------------------------
r2565 | andres | 2008-01-18 08:16:36 -0500 (Fri, 18 Jan 2008) | 5 lines

Bugfix:
    The Makefile.local from the previous revision contained extra
    definitions for clean using ::, but Makefile.in did not. This
    rendered make useless. The problem is being fixed here.

------------------------------------------------------------------------
r2564 | andres | 2008-01-18 08:14:12 -0500 (Fri, 18 Jan 2008) | 4 lines

New Features:
    Added the utility program randomTree to generate random trees,
    in newick format, with branch lengths. Used for simulations.

------------------------------------------------------------------------
r2562 | vinh | 2008-01-17 22:07:00 -0500 (Thu, 17 Jan 2008) | 3 lines

Improvement:
	Continue working on iterative pass for chromosome characters

------------------------------------------------------------------------
r2560 | andres | 2008-01-17 18:23:35 -0500 (Thu, 17 Jan 2008) | 3 lines

Improvements:
    Added the windows parallel version to the compilation rules.

------------------------------------------------------------------------
r2558 | andres | 2008-01-17 18:00:16 -0500 (Thu, 17 Jan 2008) | 6 lines

Bugfix:
    Symptom: A test of cd and pwd fails with no apparent reason.
    Problem: The path is different in each machine being tested, therefore there
    is no good reference file to compare with.
    Solution: Remove the reference file.

------------------------------------------------------------------------
r2556 | andres | 2008-01-17 17:51:53 -0500 (Thu, 17 Jan 2008) | 6 lines

Bugfix:
    Symptom: Test search07.poy fails.
    Problem: We don't filter non-unionable characters before calling 
    auto_sequence_partition and auto_static_approx.
    Solution: Filter them out!

------------------------------------------------------------------------
r2553 | andres | 2008-01-17 14:33:34 -0500 (Thu, 17 Jan 2008) | 15 lines

Bugfix:
    Symptom:
        Windows paths appear not to work properly and behave in strange manners
        (like duplicating slashes when using ctrl-p) (ncurses interface).
    Problem:
        We worked around the slash problem as a scape character in the lexer by
        escaping the individual characters. However, we are using now a special
        purpose lexer that ignores escape sequences, and therefore, there is no
        need to escape the slashes anymore.
        In addition, we did not use a special character separator between unix
        and win32.
    Solution:
        Pick the correct path separator according to the OS, and eliminate the
        character escaping functions from the command line history in ncurses.

------------------------------------------------------------------------
r2551 | ilya | 2008-01-16 14:18:02 -0500 (Wed, 16 Jan 2008) | 12 lines

Documentation Update:
    - Made substantial improvements and corrections
      to the following documents:
      - commands.tex
      - allcommands.tex
      - QuickStart.tex
      - poyheuristics.tex
      - poytutorials.tex
    - Added a new figure and corrected an existing
      figure for the 'Simple Search' section of the
      QuickStart.tex

------------------------------------------------------------------------
r2550 | andres | 2008-01-15 12:22:53 -0500 (Tue, 15 Jan 2008) | 7 lines

Improvements:
    Fixed the compilation procedures for Windows by removing the unelegant
    steps. 

    Updated the source version of PDCurses to 3.3 (we where using 2.8). This
    improves performance and overall experience for the end users.

------------------------------------------------------------------------
r2549 | andres | 2008-01-14 15:00:23 -0500 (Mon, 14 Jan 2008) | 3 lines

Bugfix:
    Corrected a syntax error that did not permit compilation in OCaml 3.10.1.

------------------------------------------------------------------------
r2548 | andres | 2008-01-13 17:06:55 -0500 (Sun, 13 Jan 2008) | 4 lines

Bugfix:
    Added some more missing test reference files, and updated the error message
    of a test to match better the characteristics of the test.

------------------------------------------------------------------------
r2547 | andres | 2008-01-12 14:01:32 -0500 (Sat, 12 Jan 2008) | 4 lines

Improvements:
    Replaced the poy_test program configuration from the readline to
    the flat interface.

------------------------------------------------------------------------
r2546 | andres | 2008-01-12 13:56:58 -0500 (Sat, 12 Jan 2008) | 5 lines

Improvements:
    Placed the LIBS environment at the end of every compilation rule which
    needed it to eliminate compile-time errors due to undefined symbols (gcc's
    linking sensibility). This was particularly important under windows.

------------------------------------------------------------------------
r2545 | andres | 2008-01-11 16:08:40 -0500 (Fri, 11 Jan 2008) | 2 lines

Reverting changes from revision 2544 which where made by mistake.

------------------------------------------------------------------------
r2544 | andres | 2008-01-11 16:07:44 -0500 (Fri, 11 Jan 2008) | 3 lines

Improvements:
    Added the --with-ocaml-flags option to pass options for the OCaml compilers.

------------------------------------------------------------------------
r2543 | andres | 2008-01-11 16:07:08 -0500 (Fri, 11 Jan 2008) | 3 lines

Improvements:
    Upon failure, during a test, the exception is raised not hidden.

------------------------------------------------------------------------
r2542 | andres | 2008-01-11 11:35:17 -0500 (Fri, 11 Jan 2008) | 10 lines

Bugfix:
    Symptom:
        No test successfully sends a reporting email.
    Problem:
        The recipient list should be extracted from the email header, however
        the -t flag is missing from the sendmail command (this is required to
        extract the recipient list).
    Solution:
        Add the -t flag in every sendmail call.

------------------------------------------------------------------------
r2541 | andres | 2008-01-11 11:34:07 -0500 (Fri, 11 Jan 2008) | 11 lines

Bugfix:
    Symptom: 
        make poy_test fails with an unresolved dependency.
    Problem:
        status.ml is preprocesses by Camlp4, which means that it is filtered
        from the default dependency check list. However, when it is included
        back for dependency generation using Camlp4 as preprocessor, the mli is
        not added again.
    Solution:
        Append status.mli to the dependency generation list after scripting.mli

------------------------------------------------------------------------
r2540 | andres | 2008-01-11 10:57:01 -0500 (Fri, 11 Jan 2008) | 4 lines

Improvements:
    The log cleanup step of run_test will now eliminate not only test_all.xml
    but all the process-specific logs.

------------------------------------------------------------------------
r2539 | andres | 2008-01-11 10:55:25 -0500 (Fri, 11 Jan 2008) | 3 lines

Bugfixes:
    Fixed the new application tests so that they can be executed successfully.

------------------------------------------------------------------------
r2537 | megan | 2008-01-10 19:20:02 -0500 (Thu, 10 Jan 2008) | 4 lines

Tests Update:
    Added missing data files gen5bp, gen11bp, gen20bp, Inv1.fas, Inv2.fas,
    ua15.fas and the test file ann.

------------------------------------------------------------------------
r2535 | megan | 2008-01-10 09:05:04 -0500 (Thu, 10 Jan 2008) | 4 lines

Documentation:
    Added description of iterative pass for chromosome characters and expanded
    description of iterative pass in set command

------------------------------------------------------------------------
r2534 | megan | 2008-01-10 08:53:28 -0500 (Thu, 10 Jan 2008) | 3 lines

Tests Update:
    Added test file "addons" with ci, ri, fasta and true cost tests 

------------------------------------------------------------------------
r2533 | megan | 2008-01-10 08:40:40 -0500 (Thu, 10 Jan 2008) | 3 lines

Test update:
    Added the test files ua_inv2.fas, gen, and unann

------------------------------------------------------------------------
r2532 | andres | 2008-01-09 09:36:18 -0500 (Wed, 09 Jan 2008) | 7 lines

Improvements:
    Added support for concurrent test execution. Now a list of tests can be run
    in parallel in multiple processors of the same machine.

    The run_test.sh script now requires a fourth argument specifying the number
    of processors to be used in the batch of tests.

------------------------------------------------------------------------
r2531 | andres | 2008-01-08 22:19:17 -0500 (Tue, 08 Jan 2008) | 5 lines

Bugfix:
    Updated the Makefile.in to handle properly USEWIN32 != true as opposed to 
    USEWIN32 == false (which is never set). This bug was introduced during the
    latest changes to properly execute the configure scripts in windows.

------------------------------------------------------------------------
r2530 | andres | 2008-01-08 22:17:04 -0500 (Tue, 08 Jan 2008) | 6 lines

Improvements:
    Ported the tests to run properly in windows.

    Multiple minor improvements to execute the tests and configuration scripts
    in windows.

------------------------------------------------------------------------
r2529 | andres | 2008-01-08 18:00:58 -0500 (Tue, 08 Jan 2008) | 5 lines

Improvements:
    Cleanup the *.win32 files that are not required anymore
    Update the win32_build.sh script for the new compilation procedures under
    windows.

------------------------------------------------------------------------
r2528 | andres | 2008-01-08 17:55:05 -0500 (Tue, 08 Jan 2008) | 4 lines

Updated support for configuration and compilation scripts under windows. 

Updated version.ml to recognize properly the html interface flags.

------------------------------------------------------------------------
r2527 | andres | 2008-01-08 16:59:52 -0500 (Tue, 08 Jan 2008) | 4 lines

Improvements:
    First changes towards configuration scripts for windows (to automate tests
    in that platform too).

------------------------------------------------------------------------
r2525 | andres | 2008-01-08 16:31:58 -0500 (Tue, 08 Jan 2008) | 4 lines

Bugfix:
    Typo in the previous modification of status_flat.ml, modifying a function
    name by mistake.

------------------------------------------------------------------------
r2524 | andres | 2008-01-08 16:26:47 -0500 (Tue, 08 Jan 2008) | 6 lines

Improvements:
    Fixed the version message to include the flat interface.

    Added help information in the configuration scripts to support the flat
    interface.

------------------------------------------------------------------------
r2523 | andres | 2008-01-08 15:51:44 -0500 (Tue, 08 Jan 2008) | 5 lines

New Features:
    Activated again the flat interface option, which removes the dependencies
    both in ncurses and readline. This is needed to activate the tests in the
    win32 platform.

------------------------------------------------------------------------
r2522 | andres | 2008-01-08 13:57:28 -0500 (Tue, 08 Jan 2008) | 3 lines

Improvements:
    Added the Makefile.win32 for graphps which was missing.

------------------------------------------------------------------------
r2521 | andres | 2008-01-08 13:48:14 -0500 (Tue, 08 Jan 2008) | 5 lines

Bugfix:
    The compilation of win32 binaries was broken as the latests changes in
    Makefile.in had not been reflected in Makefile.win32. This has been
    corrected now.

------------------------------------------------------------------------
r2518 | andres | 2008-01-07 17:44:45 -0500 (Mon, 07 Jan 2008) | 13 lines

Bugfix:
    Symptom: Issue #22
    Problem: We don't keep the gap_opening cost anywhere, nor properly assign
    the tcm name within the character specification.
    Solution: Store the information in the necessary data structure.

Interface Changes:
    Added the Tags.Characters.gap_opening tag.
    
Other Changes:
    Replaced the assignment of tcm name from "Default" to "tcm:(1,2)" which is
    properly documented.

------------------------------------------------------------------------
r2517 | andres | 2008-01-07 16:01:34 -0500 (Mon, 07 Jan 2008) | 5 lines

Bugfix:
    Symptom: Issue #18 (Ilya Temkin).
    Problem: We don't filter out the ignored terminals.
    Solution: Filter out ignored terminals.

------------------------------------------------------------------------
r2516 | andres | 2008-01-07 15:24:52 -0500 (Mon, 07 Jan 2008) | 11 lines

Bugfix:
    Symptom:
        Using additive characters uses an unbounded ammount of memory (Fernando
        Marques).
        
    Problem:
        A line of code was duplicated, causing a double allocation and the
        effective loss of the memory allocated in one of the calls.

    Solution: Delete the line responsible.

------------------------------------------------------------------------
r2515 | andres | 2008-01-06 19:43:41 -0500 (Sun, 06 Jan 2008) | 11 lines

Improvements:

Added the Scripting.Make.PhyloTree interface to simplify external scripts.

New Features:
report -> ci[:identifier]
report -> ri[:identifier]

Report the ci and ri indexes for individual characters (if the identifiers are
specified), or for the full trees (if no identifiers are specified).

------------------------------------------------------------------------
r2514 | andres | 2008-01-06 19:31:12 -0500 (Sun, 06 Jan 2008) | 5 lines

Improvements:
    Added when missing and fixed bugs and definitions in the minimum possible
    and maximum possible cost of sets of non-additive, additve, and sankoff
    characters.

------------------------------------------------------------------------
r2513 | andres | 2008-01-06 19:29:41 -0500 (Sun, 06 Jan 2008) | 4 lines

Interface Improvements:
    Added the Data.apply_on_static function, which will be used for ri and ci
    computations.

------------------------------------------------------------------------
r2512 | andres | 2008-01-06 19:28:16 -0500 (Sun, 06 Jan 2008) | 9 lines

Interface Improvements:

Added three new functions  to the Ptree module:

post_order_downpass_style 
get_roots 
extract_bremer 


------------------------------------------------------------------------
r2511 | andres | 2008-01-06 12:52:43 -0500 (Sun, 06 Jan 2008) | 7 lines

Inteface Changes:
    The to_list function of the C interface for non-additive characters returns
    a dummy cost of 1., as we don't keep the cost of each individual character
    within the vector of characters. This value is non desirable for the actual
    use of the list produced, therefore, I'm changing it to 0. too simplify the
    computation of character indexes (ci and ri).

------------------------------------------------------------------------
r2509 | vinh | 2007-12-29 10:21:41 -0500 (Sat, 29 Dec 2007) | 2 lines

Continue working on iterative pass for chrom and genome characters

------------------------------------------------------------------------
r2507 | vinh | 2007-12-28 11:40:54 -0500 (Fri, 28 Dec 2007) | 3 lines

Improvement:
    Change the default value of max_3d_len from 200 to max_int

------------------------------------------------------------------------
r2502 | ilya | 2007-12-27 10:49:20 -0500 (Thu, 27 Dec 2007) | 4 lines

Documentation Update:
    - Corrected multiple minor errors and syntactic inconsistencies
      in the 'QuickStart.tex' and 'allcommands.tex' files.

------------------------------------------------------------------------
r2500 | vinh | 2007-12-26 10:41:21 -0500 (Wed, 26 Dec 2007) | 6 lines

Improvement:
    Parameter "max_3d_len" is added which is the maximum 
    sequence length to align 3 sequences in order to
    reduce the time consuming for iterative pass for chromosomes.


------------------------------------------------------------------------
r2498 | vinh | 2007-12-21 10:54:13 -0500 (Fri, 21 Dec 2007) | 2 lines

Continue working on iterative pass for genome character

------------------------------------------------------------------------
r2496 | vinh | 2007-12-20 12:34:01 -0500 (Thu, 20 Dec 2007) | 5 lines

Improvement:
    Finished the iterative pass for chromosome character. Working on 
    iterative pass for genome


------------------------------------------------------------------------
r2494 | vinh | 2007-12-13 13:13:21 -0500 (Thu, 13 Dec 2007) | 3 lines

Improvement:
    The first version of comprehensive iterative pass for chromosome character

------------------------------------------------------------------------
r2491 | vinh | 2007-11-27 14:17:56 -0500 (Tue, 27 Nov 2007) | 3 lines

Improvement:
    The first version of exhausive iterative pass for breakinv and annotated characters

------------------------------------------------------------------------
r2489 | vinh | 2007-11-27 14:11:57 -0500 (Tue, 27 Nov 2007) | 6 lines

Improvement:
    Add an optional parameter first_gap into align_3 and readjust_3 functions
    in the sequence modul which indicates that if the first characters of 
    three are gaps or not. If not, a gap will be inserted into sequences before     aligning them


------------------------------------------------------------------------
r2488 | megan | 2007-11-27 14:11:06 -0500 (Tue, 27 Nov 2007) | 3 lines

Documentation:
    Updated references in poylibrary.bib

------------------------------------------------------------------------
r2486 | megan | 2007-11-27 11:00:34 -0500 (Tue, 27 Nov 2007) | 4 lines

Documentation:
    Edited allcommands from join method on, tutorials, and heuristic guide


------------------------------------------------------------------------
r2484 | ilya | 2007-11-26 22:03:40 -0500 (Mon, 26 Nov 2007) | 7 lines

Documentation Update:
    Numerous improvements to the documentation files:
    - QuickStart.tex
    - commands.tex
    - allcommands.tex
    - poytutorials.tex 

------------------------------------------------------------------------
r2483 | andres | 2007-11-26 18:57:00 -0500 (Mon, 26 Nov 2007) | 10 lines

Bugfix:
    Symptom:
        save ("filename") fails under MS Windows.

    Problem:
        We don't open a binary but a text channel, which fails under windows.

    Solution:
        Replace open_in and open_out with open_in_bin and open_out_bin.

------------------------------------------------------------------------
r2482 | ilya | 2007-11-20 18:54:13 -0500 (Tue, 20 Nov 2007) | 3 lines

Documentation Update:
    - Corrected the heading of the Heuristic Guide chapter

------------------------------------------------------------------------
r2481 | andres | 2007-11-20 18:06:40 -0500 (Tue, 20 Nov 2007) | 7 lines

Improvements:
    Added functions to the AddCS and NonaddCS modules for minimum and maximum
    cost of a character.

    Modified the Makefile to properly fill the new dependency between AddCS and
    NonaddCS.

------------------------------------------------------------------------
r2480 | andres | 2007-11-20 18:03:46 -0500 (Tue, 20 Nov 2007) | 12 lines

Bugfix:

    Symptom:
        read (prealigned:("x", y)) does not work when run from a script.

    Problem:
        The script analyzer ignores the `Prealigned constructor by mistake,
        eliminating the command after analyzing the script.

    Solution:
        Add the propre handling of the `Prealigned case in the script analyzer.

------------------------------------------------------------------------
r2479 | ilya | 2007-11-20 17:35:01 -0500 (Tue, 20 Nov 2007) | 4 lines

Documentation Update:
    - Numerous minor changes in the documentation formating, command
      description, and grammar.

------------------------------------------------------------------------
r2477 | megan | 2007-11-20 13:26:42 -0500 (Tue, 20 Nov 2007) | 3 lines

Documentation:
    Incorporated edits of Ward Wheeler to QuickStart.tex

------------------------------------------------------------------------
r2476 | megan | 2007-11-20 13:25:16 -0500 (Tue, 20 Nov 2007) | 3 lines

Documentation:
    incorporated edits from Ward Wheeler on allcommand document

------------------------------------------------------------------------
r2473 | vinh | 2007-11-19 16:15:31 -0500 (Mon, 19 Nov 2007) | 9 lines

Bug fixed:
    Syndrom: The iterative pass does not improve the tree 
    Problem: The cost of the tree was calculated from unadjusted tree
             instead of adjusted tree (see function 
                                      adjust_until_nothing_changes)

    Solution: The cost of the tree is calculated from the adjusted tree


------------------------------------------------------------------------
r2471 | andres | 2007-11-18 08:42:56 -0500 (Sun, 18 Nov 2007) | 12 lines

Bugfix:
    Symptom:
        ./configure --enable-long-sequence fails in the compilation step of the
        sequence.ml module (Ward Wheeler)

    Problem:
        The new split function in Sequence does not have proper type conversion
        for the different sequence lengths between Int32 and int.

    Solution:
        Do the proper conversions.

------------------------------------------------------------------------
r2466 | andres | 2007-11-13 14:05:56 -0500 (Tue, 13 Nov 2007) | 7 lines

Bugfix:
    Added the configuration environment DOCSTRING to generate the proper
    document version number for echo depending on the OS version being used.
    Leopard does recognize \n in an echo string as a newline, but linux and
    Tiger doesn't so we escape the \ in leopard while we don't for the rest.


------------------------------------------------------------------------
r2464 | megan | 2007-11-13 12:10:00 -0500 (Tue, 13 Nov 2007) | 3 lines

Documentation:
    Updated Bremer Tutorial to reflect error noted by Paola

------------------------------------------------------------------------
r2463 | andres | 2007-11-12 18:17:38 -0500 (Mon, 12 Nov 2007) | 4 lines

Improvements:
    Modified the automated building scripts to use not the hardcoded URL, but
    the MACHOST environment variable.

------------------------------------------------------------------------
r2461 | andres | 2007-11-12 18:03:14 -0500 (Mon, 12 Nov 2007) | 4 lines

Bugfix:
    Removed some debugging messages left behind for the new sequence_partition
    command.

------------------------------------------------------------------------
r2460 | ilya | 2007-11-12 15:39:12 -0500 (Mon, 12 Nov 2007) | 3 lines

Tests Update:
    - commited several changes to test scripts.

------------------------------------------------------------------------
r2458 | andres | 2007-11-10 09:33:12 -0500 (Sat, 10 Nov 2007) | 7 lines

Bugfixes:
    Various small bugfixes in the sequence_partition function.

Improvements:
    Added assertion checking in the Sequence.split function to catch illegal
    splits quickly.

------------------------------------------------------------------------
r2456 | megan | 2007-11-09 21:09:56 -0500 (Fri, 09 Nov 2007) | 3 lines

Testing:
    Updated test files within transform, fuse, build, report

------------------------------------------------------------------------
r2455 | megan | 2007-11-09 21:01:56 -0500 (Fri, 09 Nov 2007) | 3 lines

Testing:
    updated test lines in megan_tests

------------------------------------------------------------------------
r2453 | andres | 2007-11-09 17:43:54 -0500 (Fri, 09 Nov 2007) | 17 lines

New Command:

report -> fasta
report -> treecosts

See the program documentation for further information.

Documentation Fix:

    The specification of implied_alignment and ia was incorrect. Replaced the
    value of the argument from poysstring to identifiers.

Interface Changes:
    Added another argument to Implied_Alignments to include a boolean for
    whether or not a header should be included in the output (for the fasta
    functionality).

------------------------------------------------------------------------
r2452 | andres | 2007-11-09 17:41:33 -0500 (Fri, 09 Nov 2007) | 4 lines

Bugfix:
    Improved the Makefile.in rules to be able to compile the documentation in
    Mac OS X Leopard and POSIX compilant systems.

------------------------------------------------------------------------
r2451 | andres | 2007-11-09 17:30:31 -0500 (Fri, 09 Nov 2007) | 4 lines

Bugfix:
    Removed a bogus pseudorandom number generator initialization call in the
    main module.

------------------------------------------------------------------------
r2449 | andres | 2007-11-09 17:24:34 -0500 (Fri, 09 Nov 2007) | 12 lines

New Command:

transform -> sequence_partition:INT

See the program documentation for further information.

Interface changes: 
    Modified Automatic_Sequence_Partition to include a third argument holding
    an optional number of fragments. If no fragments are requested, then the
    function partitions automatically, otherwise, it will just break in as many
    fragments are requested.

------------------------------------------------------------------------
r2446 | andres | 2007-11-09 17:09:00 -0500 (Fri, 09 Nov 2007) | 3 lines

Improvements:
    The test script will now report errors to Vinh, Megan, Ilya, and Andres.

------------------------------------------------------------------------
r2444 | megan | 2007-11-08 10:59:37 -0500 (Thu, 08 Nov 2007) | 3 lines

Tutorials:
    Added 28s.aln file to tutorial_data folder

------------------------------------------------------------------------
r2442 | megan | 2007-11-08 10:43:14 -0500 (Thu, 08 Nov 2007) | 3 lines

Documentation:
    Updated tutorials (designated input files)

------------------------------------------------------------------------
r2441 | megan | 2007-11-08 10:27:18 -0500 (Thu, 08 Nov 2007) | 5 lines

Testing:
    Added transform test script folder
Tutorials:
    Added tutorial_data folder with data and scripts of all documented tutorials

------------------------------------------------------------------------
r2440 | megan | 2007-11-08 10:23:16 -0500 (Thu, 08 Nov 2007) | 3 lines

Testing:
    Updated test script folders build fuse and report

------------------------------------------------------------------------
r2439 | megan | 2007-11-08 10:17:05 -0500 (Thu, 08 Nov 2007) | 3 lines

Testing:
    Updated megan_test file with transform tests

------------------------------------------------------------------------
r2438 | andres | 2007-11-08 09:17:51 -0500 (Thu, 08 Nov 2007) | 18 lines

Bugfix:
    Symptom:
        read ("1.fas")
        set (iterative)
        build (1)
        Fails with a Not_found error (Ilya Temkin, Bug # ).

    Problem:
        There is a bug in the function to convert fast three directional trees
        to one directional trees.

    Solution:
        Do not convert the trees to one direction. There is no need to do this
        anymore as we can collect the necessary chromosomal codes without the
        conversion (this was the only use of the function). 
        Therefore, there is no need to fix the bug, just replace the function
        calls.

------------------------------------------------------------------------
r2436 | ilya | 2007-11-07 21:16:24 -0500 (Wed, 07 Nov 2007) | 3 lines

Tests Update:
    - multiple modifications to test scripts

------------------------------------------------------------------------
r2434 | megan | 2007-11-06 10:55:49 -0500 (Tue, 06 Nov 2007) | 4 lines

Testing:
    Added folders build, fuse, and report with test scripts, std err std output
    and xml files.

------------------------------------------------------------------------
r2432 | megan | 2007-11-06 09:59:37 -0500 (Tue, 06 Nov 2007) | 3 lines

Testing
    added megan_tests file to run build, fuse, and report tests

------------------------------------------------------------------------
r2430 | megan | 2007-11-06 07:24:20 -0500 (Tue, 06 Nov 2007) | 3 lines

documentation:
    Revised poytutorials to reflect actual data files

------------------------------------------------------------------------
r2426 | andres | 2007-11-05 15:33:50 -0500 (Mon, 05 Nov 2007) | 6 lines

Bugfix:
    Fixed the trees for tests that where left without the taxon name
    modification of the previous row of commits (2416-2424).
    
    Updated some costs that where failing before.

------------------------------------------------------------------------
r2425 | andres | 2007-11-05 14:41:56 -0500 (Mon, 05 Nov 2007) | 16 lines

Bugfix:
    Symptom:
        Calculating support values for Jackknife and Bootstrap could have
        incorrect results (Mark Simmons).

    Problem:
        The classifier of characters was ignoring the weight for certain kinds
        of characters, causing an overall incorrect tree cost that was only
        noticeable during jackknife and bootstrap computations. Regular analyses
        where affected, but almost nobody uses complex weighting schemes with
        weights equal to 0.

    Solution:
        Take into consideration the weight in the character and do not ignore
        characters with weight 0 comparison.

------------------------------------------------------------------------
r2422 | ilya | 2007-11-01 13:30:42 -0400 (Thu, 01 Nov 2007) | 5 lines

Tests Update:
    - Tests are committed for 'perturb', 'swap', 'search', 'set', and
      accessory commands (such as 'run', 'echo', etc.) and were placed
      in folders with corresponding names

------------------------------------------------------------------------
r2421 | ilya | 2007-11-01 13:25:50 -0400 (Thu, 01 Nov 2007) | 4 lines

Tests Update:
    - Ilya's scripts committed. They are all contained in the file
      "ilya_scripts"

------------------------------------------------------------------------
r2420 | ilya | 2007-11-01 13:14:04 -0400 (Thu, 01 Nov 2007) | 4 lines

Tests Update:
    - Corrected terminal names in .ss files by changing the "T" to "t"
      in the prefix.

------------------------------------------------------------------------
r2419 | ilya | 2007-11-01 13:11:42 -0400 (Thu, 01 Nov 2007) | 5 lines

Tests Update:
    - Changed terminal names in the remaining datafiles (.san, .aa) by adding
      a prefix "t" to make it consistent with Hennig86 file format requiring
      sung letters for taxon names.

------------------------------------------------------------------------
r2418 | ilya | 2007-11-01 13:07:21 -0400 (Thu, 01 Nov 2007) | 5 lines

Tests Update:
    - Corrested terminal names in all fas files: added a prefix "t"
      to each terminal name to make is consistent with Hennig86
      requirement for taxon names

------------------------------------------------------------------------
r2416 | vinh | 2007-11-01 10:40:51 -0400 (Thu, 01 Nov 2007) | 5 lines

Improvement:
    Using Sequence.align2 to align two general character sequences
    instead of Ocaml's function


------------------------------------------------------------------------
r2407 | megan | 2007-10-25 14:51:29 -0400 (Thu, 25 Oct 2007) | 3 lines

Documentation:
    -revised the Bremmer tutorial

------------------------------------------------------------------------
r2405 | andres | 2007-10-25 14:07:00 -0400 (Thu, 25 Oct 2007) | 5 lines

Improvements:
    Removed the recomputation of trees and interior states from saved and loaded
    trees to improve overall performance and be able to use the feature within
    scripts without hitting the speed of the application.

------------------------------------------------------------------------
r2402 | vinh | 2007-10-25 13:21:28 -0400 (Thu, 25 Oct 2007) | 6 lines

Bug fixed:
    Syndrom: Create an empty single genome
    Problem: The single state for a single node is empty
    Solution: Fix it, if it's a single node, then return its own genomes


------------------------------------------------------------------------
r2401 | andres | 2007-10-24 15:09:17 -0400 (Wed, 24 Oct 2007) | 11 lines

Bugfix:
    Symptom:
        build (random) select () could fail with an AllDirNode.is_collapsible
        failure.

    Problem:    
        We don't do uppass on random trees.

    Solution:
        Add the necessary uppass evaluations.

------------------------------------------------------------------------
r2399 | andres | 2007-10-24 11:34:07 -0400 (Wed, 24 Oct 2007) | 14 lines

Bugfix:
    Symptoms: 
        echo ("%") would cause the program to crash.
        Issue #11 (Paola Pedraza).

    Problem:
        % and @ are special formatting characters, and they are not properly
        % escaped.

    Solution:
        Escape every user-provided string that is to be used in printed output.



------------------------------------------------------------------------


------------------------------------------------------------------------
r2397 | ilya | 2007-10-23 15:55:09 -0400 (Tue, 23 Oct 2007) | 6 lines

Documentation Update:
    - Included a substitute figure for the title page;
    - Make numerous improvements to the QuickStart.tex;
    - Corrected formatting of TOC and the link to Google
      Repository in 'commands.tex'

------------------------------------------------------------------------
r2392 | andres | 2007-10-23 10:42:55 -0400 (Tue, 23 Oct 2007) | 16 lines

Improvements:
    Added support for store, and use trees, data, jackknife, bootstrap, or
    bremer. The feature will remain undocumented until we find some use for it
    (it's only for research purposes for now).

Bugfix:
    Symptom:
        read ("a") build (1) read ("b") does not automatically update the tree
        cost.

    Problem:
        After reading the data, we never really update the tree.

    Solution: 
        Do it!



CHANGES BETWEEN 2318 AND 2398:

Overview:

This release contains only documentation improvements and bugfixes. The parallel
execution of numerous scripts should have important performance improvements.

Details:

------------------------------------------------------------------------
r2397 | ilya | 2007-10-23 15:55:09 -0400 (Tue, 23 Oct 2007) | 6 lines

Documentation Update:
    - Included a substitute figure for the title page;
    - Make numerous improvements to the QuickStart.tex;
    - Corrected formatting of TOC and the link to Google
      Repository in 'commands.tex'

------------------------------------------------------------------------
r2392 | andres | 2007-10-23 10:42:55 -0400 (Tue, 23 Oct 2007) | 16 lines

Bugfix:
    Symptom:
        read ("a") build (1) read ("b") does not automatically update the tree
        cost.

    Problem:
        After reading the data, we never really update the tree.

    Solution: 
        Do it!

------------------------------------------------------------------------
r2388 | megan | 2007-10-23 08:21:12 -0400 (Tue, 23 Oct 2007) | 3 lines

Documentation:
    Added Annotated Chromosome and BreakInv tutorials

------------------------------------------------------------------------
r2385 | andres | 2007-10-22 17:13:38 -0400 (Mon, 22 Oct 2007) | 14 lines

Bugfix:
    Symptom:
        build (10) report (ia) merges in one long sequence, all the trees, as if
        we had 10 characters and only one tree in the implied alignment (Gonzalo
        Giribet).
    Problem:
        We do not iterate over the trees to produce the implied alignment, but
        we first compute all the implied alignments, and after merging, iterate
        to print them out, effectively merging different trees.
    Solution (Interface Change):
        Diagnosis.diagnose should accept one tree at a time, and output its
        diagnosis, for each independent tree.


------------------------------------------------------------------------
r2383 | andres | 2007-10-22 16:56:32 -0400 (Mon, 22 Oct 2007) | 4 lines

Improvements:
    Several improvement to reduce bad decision making when attempting to
    optimize a script.

------------------------------------------------------------------------
r2382 | megan | 2007-10-22 11:46:34 -0400 (Mon, 22 Oct 2007) | 3 lines

Documentation:
    Updated Bremer Tutorial with visited strategy

------------------------------------------------------------------------
r2381 | andres | 2007-10-20 14:21:21 -0400 (Sat, 20 Oct 2007) | 5 lines

Bugfix:
    Removed the thread index of the skip command automatically added by the
    analyzer, to avoid filling a bogus dependency (and possibly erroneous)
    dependency to an empty command (aka. Skip).

------------------------------------------------------------------------
r2380 | andres | 2007-10-20 11:09:58 -0400 (Sat, 20 Oct 2007) | 3 lines

Bugfix: 
    Removed a directory name that caused a bogus test failure.

------------------------------------------------------------------------
r2378 | andres | 2007-10-19 17:48:35 -0400 (Fri, 19 Oct 2007) | 3 lines

Improvements:
    Added tests for the analyzer using the tutorial scripts. 

------------------------------------------------------------------------
r2374 | andres | 2007-10-19 16:42:04 -0400 (Fri, 19 Oct 2007) | 9 lines

Improvements:
    Added rules to properly compose Parallelizable operations and be able
    to extend pipelines, even if we hit a non composable operation after a
    sequence of composable parallelizable functions.

Bugfix:
    Replaced Build_Random with Build in the type Analyzer.all_methods. This was
    a typo in the previous commit.

------------------------------------------------------------------------
r2371 | andres | 2007-10-19 15:15:43 -0400 (Fri, 19 Oct 2007) | 4 lines

Improvements:
    Added a nice error message when the user attempts to set an invalid terminal
    as root. This resolves issue 10.

------------------------------------------------------------------------
r2369 | andres | 2007-10-19 15:00:31 -0400 (Fri, 19 Oct 2007) | 21 lines

Improvements:
    - Parallelized build (constraint)
    - Added parallelization support for many simple cases that where not
      parallelized before (for instace build (10) transform (static_approx)
      build (10)).

Bugfix:
    Symptom:
        build (2) build (3)  builds in total 6 trees instead of 5 as expected.
    Problem:
        The parallel operations between builds are pipelined, causing a
        multiplicative effect.

    Solution:
        Verify the kind of compositions intended between Parallelizable
        commands.

Interface Changes:
    Added the `Skip command, which does ... nothing. A placeholder useful for
    the script analyzer.

------------------------------------------------------------------------
r2364 | andres | 2007-10-18 16:16:28 -0400 (Thu, 18 Oct 2007) | 3 lines

Improvements:
    Now filter characters with weight 0.

------------------------------------------------------------------------
r2363 | ilya | 2007-10-18 16:15:29 -0400 (Thu, 18 Oct 2007) | 5 lines

Documentation Update:
    - Included Sensitivity Analysis tutorial ('poytutorials.tex');
    - Improved formatting of 'poytutorials.tex';
    - Corrected the title of the front page ('commands.tex')

------------------------------------------------------------------------
r2361 | andres | 2007-10-18 16:03:26 -0400 (Thu, 18 Oct 2007) | 20 lines

Improvements:
    
    - Added the NonaddCS.is_potentially_informative, and
      AddCS.is_potentially_informative to verify if a set of observations is
      could produce a tree with cost greater than 0.

    - Added Data.apply_bool to apply a bolean function only to certain
      characters (currently only additive or nonadditive), without the need of
      unwrapping the Data.d structure.

    - Modified the Jackknife support calculation. Instead of selecting a certain
      fraction of characters, each character is assigned weight 0 with the
      selected probability of remotion to allow the computation of support
      values with very few characters (and the easy verification of small
      examples).

    - Removed an error that was raised when very few characters existed to
      compute a reasonable Jackknife.


------------------------------------------------------------------------
r2358 | megan | 2007-10-18 11:42:28 -0400 (Thu, 18 Oct 2007) | 3 lines

Added documentation:
    - tutorial for ("Genome Analysis")

------------------------------------------------------------------------
r2355 | megan | 2007-10-18 07:46:33 -0400 (Thu, 18 Oct 2007) | 3 lines

Added:
Annotated chromosome tutorial (mt data set)

------------------------------------------------------------------------
r2354 | megan | 2007-10-17 20:53:53 -0400 (Wed, 17 Oct 2007) | 4 lines

Created new Bremer Support tutorial using dynamic characters
Created new Jackknife Support tutorial using static characters


------------------------------------------------------------------------
r2351 | vinh | 2007-10-17 17:46:32 -0400 (Wed, 17 Oct 2007) | 8 lines

Bug fixed:
    Syndrom: Crashed with annotated chromosomes
    Problem: The complement code of "*" (code=31) is zero 
             which is an illegal code.

    Solution: Change complement of gap is gap, of "*" is "*", of "?" is "?"


------------------------------------------------------------------------
r2349 | andres | 2007-10-17 17:13:55 -0400 (Wed, 17 Oct 2007) | 13 lines

Bugfix:
    
    Symptom:
        read ("chel.aln") build (1) transform (auto_sequence_partition) 
        transform (auto_sequence_partition) .... (* repeat n times *) decreases
        the overall tree cost.

    Problem:
        Sequence.split removes the tail of the last resulting sequence.

    Solution:
        Don't extract len - 1 but len elements from the last sequence.

------------------------------------------------------------------------
r2348 | andres | 2007-10-17 16:36:40 -0400 (Wed, 17 Oct 2007) | 13 lines

Bugfix:
    Symptom:
        read ("fasta") build (1) transform (static_approx) report (phastwinclad)
        fails with a Data.get_alphabet error.

    Problem:
        There is a duplicated function: Data.get_alphabet, with an old and a new
        definition. The old definition did not handle static homology
        characters.

    Solution:
        Eliminate the old definition of Data.get_alphabet.

------------------------------------------------------------------------
r2346 | andres | 2007-10-17 16:21:35 -0400 (Wed, 17 Oct 2007) | 14 lines

Bugfix:
    Symptom:
        A script containing store instructions ignores the instructions. The
        named stores do not appear when used once the script is finished.

    Problem:
        The analyzer automatically cleans up unused stored program states,
        including not only the internal program stored states, but also the
        user stored states, which might be used in the unknown future.

    Solution:
        Only remove the internal states of the program (those with prefix __poy
        in the name).

------------------------------------------------------------------------
r2344 | andres | 2007-10-17 15:34:40 -0400 (Wed, 17 Oct 2007) | 4 lines

Improvements:
    Added the -error flag to the Test_line program to expect an abnormal program
    termination in the poy_test execution of a test line.

------------------------------------------------------------------------
r2342 | ilya | 2007-10-17 12:13:08 -0400 (Wed, 17 Oct 2007) | 6 lines

Documentation Update:
    - Corrected the addresses and names of authors ('commands.tex');
    - Expanded comments for 'iterative' argument of 'set' ('allcommands.tex');
    - Completed tutorial 2 ('Searching under Iterative Pass')
      ('poytutorials.tex')

------------------------------------------------------------------------
r2340 | andres | 2007-10-17 08:36:09 -0400 (Wed, 17 Oct 2007) | 19 lines

Bugfix:
    Symptom: 
        report ("file", trees:(nomargin)) fails to produce any output (Christian
        Kehlmaier).

    Problem:
        Changing the margin size of the pretty printer causes the current output not
        to be properly flushed from the pretty printer (an OCaml bug?).

    Solution (Workaround):
        Check if the marging is changing, if it is, flush the formater before
        continuing printing.

Interface Changes:
    Modified the command nomargin. Instead of setting the margin to max_int, it
    sets it to the maximum stored in OCaml Format module, to be able to
    recognize if the margin has not changed when normargin is set.


------------------------------------------------------------------------
r2338 | andres | 2007-10-16 17:56:06 -0400 (Tue, 16 Oct 2007) | 16 lines

Bugfix:

    Fix issue 8.
    Symptom: 
        Calculate bremer support with a small number of random addition
        sequences per clade shows infinite support values (Mark Simmons).

    Problem:
        We use the IEEE infinity to represent bad tree costs. However, the
        comparsion of infinities and their diferences cause incorrect
        calculations.

    Solution:
        Replace infinity with float_of_int max_int to maintain a high value with
        better precision in the cost comparison computations.

------------------------------------------------------------------------
r2336 | andres | 2007-10-16 13:55:31 -0400 (Tue, 16 Oct 2007) | 8 lines

Improvements:
    Fills enhancement issue request 6. POY now properly recognize small custom
    alphabet (less than 6 elements), and uses the stronger, all combination
    algorithm of Direct Optimization to optimize the alignments.

Interface Changes:
    Added Alphabet.explote. See the documentation for further information.

------------------------------------------------------------------------
r2334 | andres | 2007-10-16 11:34:50 -0400 (Tue, 16 Oct 2007) | 4 lines

Improvements:
    Changed the default xml report to test.xml and added support for the odiff
    option in test_line.ml

------------------------------------------------------------------------
r2332 | andres | 2007-10-16 10:41:09 -0400 (Tue, 16 Oct 2007) | 7 lines

Improvements:
    Updated the test scripts to handle the options -inputfile, -costfile,
    -costlessfile, -stderr, -stdout, -diff, -ostderr, -ostdout, -odiff. 

    Changed the behavior of ./poy_test -cl x to check for the tree cost being
    less than or equal to x, instead of strictly less than x.

------------------------------------------------------------------------
r2330 | andres | 2007-10-15 14:44:31 -0400 (Mon, 15 Oct 2007) | 8 lines

Improvements:
    Improved the support calculation algorithm to match the request in issue 2.
    After each replicate, zero length branches are collapsed in each resulting
    best tree, the strict consensus is computed, and the clades in that strict
    consensus are added to the overall counters.

    This fixes request issue 2 (Mark Simmons).

------------------------------------------------------------------------
r2328 | andres | 2007-10-15 13:44:08 -0400 (Mon, 15 Oct 2007) | 23 lines

Bugfix:
    Symptom: Issue 1. Consensus tree does not match the expected result from the
    input trees. It contains more unresolved branches than it should (Mark
    Simmons).

    Problem:
        The consensus file is correct. The problem comes from the branch
        collapsing functions, that are collapsing branches that should not be.
        The collapsing for dynamic homology characters should only use the
        single assignment, not the ambiguous assignment for Dynamic homology
        characters.

    Solution:
        Dynamic homology characters evaluate if they are or not collapsible
        using the adjusted assignment, while static homology characters use the
        final state assignment.

Interface Changes:
    Node.is_collapsable accepts an extra argument of type [`Any | `Static |
    `Dynamic ] to select the appropriate vertex state to compute the result.

    The Node.is_collapsable function calculates the distance of every Dynamic
    homology character using the standard distance as opposed to the
    tabu_distance as before.

------------------------------------------------------------------------
r2327 | ilya | 2007-10-15 13:38:58 -0400 (Mon, 15 Oct 2007) | 6 lines

Documentation Update:
    - Updated titles of figure in the 'QuickStart.tex' by
      replacing all upper-case characters with lower-case characters;
    - Includeded the tutorial for iterative pass (in 'poytutorials.tex');
      still unfinished.

------------------------------------------------------------------------
r2326 | ilya | 2007-10-15 13:27:56 -0400 (Mon, 15 Oct 2007) | 4 lines

Documentation Update:
    - Added a missing figure ('searchforbremer_menu.jpg') for
      the 'QuickStart.tex'

------------------------------------------------------------------------
r2323 | andres | 2007-10-15 11:09:06 -0400 (Mon, 15 Oct 2007) | 2 lines

Continue removing files to unify filename conventions.

------------------------------------------------------------------------
r2322 | andres | 2007-10-15 11:07:12 -0400 (Mon, 15 Oct 2007) | 2 lines

Removing all upper case names to unify filename conventions.

------------------------------------------------------------------------
r2321 | andres | 2007-10-15 10:59:00 -0400 (Mon, 15 Oct 2007) | 17 lines

Bugfixes:
    Symptom: Issue 4. Some NEXUS files fail to be loaded (Ward Wheeler).
    Problem:
        Two problems: We don't report any error message when there are illegal
        commands in the Assumtion block (in the bug report the Charset command
        inside the Assupmtion block is an illegal command for Nexus), 
        and we don't ignore spaces when attempting to read NoLabels, failing to
        recognize the end of the input, and therefore, not raising an exception
        (End_of_file) which is expected to verify the sanity of the declared
        magtrix size and true matrix size with NoLabel options in the Data
        block.

    Solution:
        Add the necessary error messages, ignore the spaces when reading nexus
        files with NoLabel, and before reporting an error, verify that we really
        have reached the last element in the matrix stream.

------------------------------------------------------------------------
r2320 | ilya | 2007-10-15 10:58:17 -0400 (Mon, 15 Oct 2007) | 3 lines

Documentation Update:
    - changed all the uppercase letters in names of figures to lower case

------------------------------------------------------------------------
r2319 | andres | 2007-10-15 09:28:07 -0400 (Mon, 15 Oct 2007) | 2 lines

Bugfix: Resolve issue #3 (http://code.google.com/p/poy4/issues/detail?id=3).
Minor cosmetic improvement.

------------------------------------------------------------------------



CHANGES BETWEEN 2205 AND 2318:

Overview:


    Command Change:
        - Replaced transform (fixedstates) with transform (fixed_states) to
          improve command naming consistency.
    General Program Behaviour:
        - Multiple improvements and bugfixes in the GUI for all platforms.
    Analysis new features and most important bug fixes:
        - Building with constraint trees is now supported (build (constraint)).
        - Building trees using branch and bound, and generating trees at random
          is now supported (build (branch_and_bound), build (random)).
        - Resolved iterative pass bug that could cause the program not to
          terminate.
        - Inversions now detect not the inverted sequence, but the inverted
          complement of the sequence.
        - New symmetric option for chromosomal characters to guarantee the
          symmetry of the distance between a pair of chromosomes (constant extra
          time complexity).
        - Changed the default value of rearranged_len from 1000 to 100
          so that we can cover smaller rearrangements
        - Changed the default value of chrom_hom from 2.0 to 0.75 to
          avoid wrong homologous statements between distantly related
          chromosomes.
    Compilation:
        - ./configure --enable-mpi does not require now the name of the mpi
          library. Just use it to enable parallel execution using MPI.

Detailed Changes:
------------------------------------------------------------------------
r2292 | ilya | 2007-10-09 12:30:44 -0400 (Tue, 09 Oct 2007) | 4 lines

Documentation Update:
    - Added explanatory statements regarding the arguments
      'seed' and 'iterative' of the command 'set'.

------------------------------------------------------------------------
r2282 | ilya | 2007-10-08 13:16:10 -0400 (Mon, 08 Oct 2007) | 4 lines


cumentation Update:
    - Improved and corrected the description of 'rename' command

------------------------------------------------------------------------
r2281 | ilya | 2007-10-08 13:15:06 -0400 (Mon, 08 Oct 2007) | 3 lines

Documentation Update:
    - Updated and corrected the description of GUI

------------------------------------------------------------------------
r2280 | ilya | 2007-10-08 13:14:01 -0400 (Mon, 08 Oct 2007) | 4 lines


Documentation Update:
    - Updated screenshots for the QuickStart

------------------------------------------------------------------------
r2277 | andres | 2007-10-06 11:54:21 -0400 (Sat, 06 Oct 2007) | 6 lines

Improvements:
    Override the default Camlp4 Lexer with a simplified lexer that ignores the
    escape sequences (with the exception of \") so that Windows and Unix users can write
    exactly the sequence of characters that they desire in the POY command line
    without needing to know anything about escape sequences.

------------------------------------------------------------------------
r2275 | andres | 2007-10-05 16:40:18 -0400 (Fri, 05 Oct 2007) | 3 lines

Improvements:
    Made the slaves quiet in parallel execution.

------------------------------------------------------------------------
r2273 | andres | 2007-10-05 11:40:27 -0400 (Fri, 05 Oct 2007) | 11 lines

Bugfix:
    Symptom: Specifying transform (gap_opening:x) for aminoacid characters could
    cause a crash (Ilya Temkin)

    Problem: The clone function for cost matrices passed the incorrect alphabet
    size for non-combination matrices.

    Solution: If the matrix is for a non-combination alphabet, do not pass the
    logarithm of the overall size of the alphabet as alphabet size, but the
    total number of elements.

------------------------------------------------------------------------
r2272 | andres | 2007-10-05 11:03:07 -0400 (Fri, 05 Oct 2007) | 30 lines

Bugfix:
    Symptom:
        swap (around) fails with an error message (Megan Harrison).

    Problem:
        We do not update properly the tabu manager inside the queue manager.

    Solution:
        Update the tabu manager after doing the joins and breaks inside the
        around queue manager.

Bugfix:
    
    Symptom:
        swap (around) may continue in an endless loop.

    Problem:
        We don't update correctly the final edge to test to continue iterating
        during the local search, leaving it as -1, reaching a loop that can never 
        finish as the edge counter must be a positive integer.
   
    Solution:
        Update the final edge position correctly.

Interface Changes:
    Modified the Ptree.alternate_spr_tbr and renamed it to Ptree.alternate, to
    accept as part of it's input the spr and tbr functions to be used in the spr
    and tbr steps.

------------------------------------------------------------------------
r2269 | andres | 2007-10-04 11:48:28 -0400 (Thu, 04 Oct 2007) | 3 lines

Improvements:
    Updated the scripts to the new --enable-mpi configuration flag.

------------------------------------------------------------------------
r2264 | vinh | 2007-10-04 08:57:13 -0400 (Thu, 04 Oct 2007) | 8 lines

Improvement:
    A dummy solution for iterative pass for chromosome characters are 
    implemented. It makes sure that the iterative pass is available for
    all characters.
    However, a comprehensive solution needs to be developed in order to 
    increase the quality of the tree

------------------------------------------------------------------------
r2263 | andres | 2007-10-03 16:51:13 -0400 (Wed, 03 Oct 2007) | 8 lines

Improvements:
    The implied alignments now merge sequences belonging to the same input
    file. The sequences are separated by a space, making them readable in other
    FASTA reading programs.

Changes:
    Removed the 80 character margin for printing out implied alignments.

------------------------------------------------------------------------
r2261 | vinh | 2007-10-03 11:19:36 -0400 (Wed, 03 Oct 2007) | 11 lines

Bug fixed:
    Symptom: The total cost in the diagnosis does not match the tree cost
    Problem: Forgot to delete the gaps 
             when calculating the cost between single sequences

    Solution: deleting the gaps before calculating

------------------------------------------------------------------------
r2260 | andres | 2007-10-03 09:00:15 -0400 (Wed, 03 Oct 2007) | 10 lines

Bugfix:
    Symptom:
        Compiling with --enable-large-alphabets fails (automated test).

    Problem: 
        A typo in the DESERIALIZE_SEQT macro left an invalid function.

    Solution:
        Correct the typo.

------------------------------------------------------------------------
r2259 | andres | 2007-10-03 08:56:31 -0400 (Wed, 03 Oct 2007) | 20 lines

New Features:

New Argument:

build -> constraint[:STRING]

    See the function documentation for further information.

------------------------------------------------------------------------
r2258 | andres | 2007-10-03 08:50:59 -0400 (Wed, 03 Oct 2007) | 4 lines

Improvements:
    Added the new wagner tabu manager Tabu.constrained_dfs_wagner for tree building under a
    certain constraint.

------------------------------------------------------------------------
r2257 | andres | 2007-10-01 18:42:46 -0400 (Mon, 01 Oct 2007) | 15 lines

Bugfix: 
    Symptom: Segmentation error when using 'inspect' (Ilya Temkin, bug 277)

    Problem: 
        The marshaling functions did not handle properly the different sequence
        representations (for long and short alphabets).

    Solution:
        Added the necessary macros in seq.h and the proper calls in cm.c and
        seq.c depending on the alphabet size.

------------------------------------------------------------------------
r2256 | andres | 2007-10-01 18:24:29 -0400 (Mon, 01 Oct 2007) | 10 lines

Bugfix:
    Symptom: 
        swap (recover) does not recover the trees when running inside a
        pipeline (Norberto Giannini).
    Problem:    
        Between commands we always clean the queue of recovered trees.
    Solution:
        Do not clean the queue. We fully depend on the user to limit the memory
        consumption of the command.

------------------------------------------------------------------------
r2253 | andres | 2007-10-01 14:23:07 -0400 (Mon, 01 Oct 2007) | 3 lines

Improvements:
    Changed fixedstates to fixed_states. This fixes bug 268.

------------------------------------------------------------------------
r2252 | andres | 2007-10-01 14:19:32 -0400 (Mon, 01 Oct 2007) | 4 lines

Bugfix:

    Symptom:
	    According to the documentation, if the filename is not
	    specified, the execution of the following command should
	    produce out put on screen:
	        echo ("print on screen", output)
	    Instead, poy detects a syntactical error (Ilya Temking, bug 279)
    Problem : We don't handle the case that is promissed in the documentation.
    Solution: Handle it!


------------------------------------------------------------------------
r2251 | andres | 2007-10-01 14:09:38 -0400 (Mon, 01 Oct 2007) | 5 lines

Improvements:

    New Command Feature:
        The ratchet parameters are now optional. This fixes request 280.

------------------------------------------------------------------------
r2249 | andres | 2007-10-01 14:04:22 -0400 (Mon, 01 Oct 2007) | 4 lines

Improvements:
    To improve consistency, run () now is an illegal command, and requires an
    argument.

------------------------------------------------------------------------
r2247 | andres | 2007-10-01 13:57:33 -0400 (Mon, 01 Oct 2007) | 5 lines

Improvements:
    Improved the behavior of search (build) according to the feature request
    285. search will now by default _build trees_.


------------------------------------------------------------------------
r2246 | andres | 2007-10-01 13:44:55 -0400 (Mon, 01 Oct 2007) | 5 lines

Bugfix:

    Symptom:
            Executing the script below issues the following error:

            Error: 
                Command error in file /Users/ilyat/Desktop/Untitled.txt 
                line 4 between characters 5 and 6 :
                [swap_argument] expected after [left_parenthesis] 
                (in [swap]) 

            The script:
                read ("FILENAME")
                build (2)
                swap(constraint:4)

            I suspect that this syntax was intended to be synonymous
            with swap(constraint:(depth:4)), which does work 
            (Ilya Temkin, bug 287).

    Problem: We don't have a rule for this case in the parser.

    Solution: Add the proper rule in the command line parser.

------------------------------------------------------------------------
r2245 | andres | 2007-10-01 13:16:23 -0400 (Mon, 01 Oct 2007) | 9 lines

Bugfix:
    Symptom:
        The arguments 'weight' and 'weightfactor' of the 'transform' command are
        properly applied (as can be seen by comparison of tree costs with and
        without weighting) but there is no corresponding report (generated
        either by 'report(data)' or outputed as XML) showing which characters
        have been transformed and what weights have been applied (Ilya Temkin,
        bug 274).

    Problem: The functionality was missing.

    Solution: Add the necessary functions.

------------------------------------------------------------------------
r2244 | vinh | 2007-09-28 08:50:24 -0400 (Fri, 28 Sep 2007) | 11 lines

Bug fixed:
    Symptom: ua2.poy failed

    Problem: costs do not match because of fixing the orientation problem 
    for chromosomes

    Solution: Changed the cost in the cost_tests

------------------------------------------------------------------------
r2241 | andres | 2007-09-24 13:38:01 -0400 (Mon, 24 Sep 2007) | 12 lines

Bugfix:
    Symptom:
        Iterative pass may never finish.
    Problem:
        The tree cost check invariant was dropped by mistake (that after each
        iterative pass the overall tree cost must have dropped).
    Solution:
        Restore the invariant check. 

------------------------------------------------------------------------
r2238 | vinh | 2007-09-21 14:09:14 -0400 (Fri, 21 Sep 2007) | 13 lines

Bug fixed:
    Symptom: 
        The misunderstanding of inversion for chromosome chracter. 
        One inversion not only reverse the order of one sequence 
        but also convert all nucleotides into their complements.
    
    Problem: 
        Inversion is not detected correctly

    Solution: 
        When convert a sequence, the nucleotides are also converted.

------------------------------------------------------------------------
r2237 | vinh | 2007-09-21 14:06:24 -0400 (Fri, 21 Sep 2007) | 6 lines

Improvement:
    Add the complement_chrom function to the sequence module.
    It is the same as complement function for sequence, 
    but no gap is inserted at the begin

------------------------------------------------------------------------
r2231 | vinh | 2007-09-19 14:40:15 -0400 (Wed, 19 Sep 2007) | 7 lines

Improvement:
    Add the symmetric option for chromosome character. If symmetric
    is set to true, the median between two chromosomes (X,Y) will
    be the best medians between (X,Y) and (Y, Z). This solves 
    the symmetric problem of chromosome characters


------------------------------------------------------------------------
r2230 | vinh | 2007-09-19 14:38:23 -0400 (Wed, 19 Sep 2007) | 10 lines

Bug fixed: impliedAlignment.ml
    Symptom: assert fail when checking if the chromosome length 
             is greater than 1 in the calculate_indels function

    Problem: the chromosome length can be 1 if it does not contain 
             any extra gap at the begin as assumed in for sequence

    Solution: Check if the first base is a gap
    

------------------------------------------------------------------------
r2229 | ilya | 2007-09-18 17:46:58 -0400 (Tue, 18 Sep 2007) | 4 lines

Documentation Update:
    - Included 'xslt' argument for the 'report'
      command in the 'allcommands.tex' document

------------------------------------------------------------------------
r2226 | andres | 2007-09-18 13:26:55 -0400 (Tue, 18 Sep 2007) | 3 lines

Improvements:
    Made the file reading procedure remote to support execution in enyo.

------------------------------------------------------------------------
r2225 | andres | 2007-09-18 13:26:21 -0400 (Tue, 18 Sep 2007) | 5 lines

Improvements:
    Moved the Status initialization functions for parallel execution from Main
    to Scripting.Make to simplify the execution of other programs using POY as
    a library.

------------------------------------------------------------------------
r2222 | andres | 2007-09-18 10:51:29 -0400 (Tue, 18 Sep 2007) | 10 lines

Bugfix:
    Symptom:
        Building a random tree fails with an "Unsupported" message.

    Problem:
        The sadman information was not added, and instead raises the exception.

    Solution:   
        Add the required sadman information.

------------------------------------------------------------------------
r2218 | andres | 2007-09-16 19:50:32 -0400 (Sun, 16 Sep 2007) | 18 lines

New Command:

New Argument:
    build -> random 
    
    See the function documentation for further information.

Bugfix:
    Symptom:
        build (branch_and_bound) may return with suboptimal trees.

    Problem:
        We use as bound for the last tree found the previous best
        cost plus the threshold.

    Solution:
        Use the new best cost plus the threshold.

------------------------------------------------------------------------
r2216 | andres | 2007-09-16 16:18:52 -0400 (Sun, 16 Sep 2007) | 9 lines

New Feature:

    Added branch and bound to the build methods. See build->branch_and_bound for
    more documentation.

New Command:
build -> branch_and_bound[:FLOAT]

------------------------------------------------------------------------
r2215 | vinh | 2007-09-14 15:41:52 -0400 (Fri, 14 Sep 2007) | 6 lines

Bug fixed:
    Symptom: could not compile
    Problem: chrom_hom was set to 0.75
    Solution: chrom_hom is set to 75 


------------------------------------------------------------------------
r2214 | vinh | 2007-09-14 14:04:39 -0400 (Fri, 14 Sep 2007) | 2 lines

Added missing default and suggested values for chromosome parameters

------------------------------------------------------------------------
r2213 | vinh | 2007-09-14 13:28:00 -0400 (Fri, 14 Sep 2007) | 3 lines

Changed to default value of chrom_hom from 2.0 to 0.71 as described 
in the documentation



CHANGES BETWEEN 1983 AND 2205:

Overview:

    General Program Behaviour:
        - Drastic improvements in memory consumption.
        - 30% speed improvement in alignment performance for windows and linux
          for alignments without gap opening (contribution of Johan Anas).
        - New GUI for Windows, Mac OS X (universal), and Linux (GTK2 - x86).
        - New Windows installers.
        - Added full support for Nexus files.
        - Added support for cname commands from WinClada/Nona/TNT files.
        - Added support for character names in input and output.
        - Added XSLT support for postprocessing POY's output. A user can now 
          write a small xslt transform and ask POY to produce, for example,
          a tree with branch lengths, or a postscript file with the table 
          format required by a particular journal in the apomorphy lists.
    Analysis Features:
        - Iterative pass for DNA sequences only.
        - Static approximation for affine gap costs produce blocks of indels as
          separate characters. As a result, the cost of a tree after static
          approx do not change drastically and heuristics can be applied without
          distorting the tree search.
        - Implied alignments and static approximation for chromosome, 
          annotated chromosome and breakinv characters.
        - New consensus-like tree generated from jackknife and bootstrap clade
          frequency counts.
    Compilation:
        - Drastic simplification of configuration and compilation steps.
        - Removed the gcc requirement. Any modern ISO 99 C compiler is enough.
        - Numerous new options in configure step (see ./configure --help).
        - POY now REQUIRES OCaml 3.10.0 for compilation.

    Many many many bugfixes. 

Detailed Changes:

Improvement:

Improvements:
    Improvements (by Johan Anas, anas.johan@gmail.com):
    30% performance improvements in intel processors under Windows and Linux OS.


Documentation Changes:
    Improved the description of select (missing)

Improvement:
    The XML output now uses prefix Ancestor and Descendant to
    distinguish the same features from ancestor and descent characters
    in the diagnosis.  For example: AncestorReferenceCode,
    DescentdantReferenceCode...
    
    
Bugfix:
    Symptom: 
        The gap code in the alphabet and cost matrix is not the same 
        for breakinv character with orientation.

    Problem: 
        Let n be the number of character states.  The alphabet size will be (2n
        + 1) instead of (2n + 2) because there is no negative gap state.

    Solution: 
        Fix the problem in the of_channel function in cost_matrix.ml

Improvements:
    Removed most taxon name constraints when reading tree files. Only ;, [, ],
    (, ), ;, and whitespaces have special meaning in terminals of an input tree.

Improvements:
    Reduced memory consumption by changing the representation of the sequences
    from arrays of integers to arrays of unsigned chars. The new macro SEQT
    defined in seq.h is the specified type for sequences. If someone wants to
    analyze datasets with alphabets larger than 255, they will have to change
    SEQT to int.

Improvements:
    Added support for various mst-based styles of build (See the Mst interface
    for more information).
    Added an option to verify the cost of a tree in the build queue managers.

Improvements:
    Removed all the remaining callse to clear_internals. Reducing memory is not
    needed anymore (not to mention that it is hardly elegant).

Change:
    1. The locus and chromosome indel calculation is changed slightly 
       to be consistent with the affine gap model as implemented for 
       DNA sequence.
       Before:
            Cost = opening cost + (number characters - 1) * extension cost

      Now:
           Cost = opemmomg cost + number character * extension cost

Bugfix:
    Symptom:
        Some auto_sequence_partition commands could fail with an assertion
        failure.

    Problem:
        Internally, the left right checking for the tree traversion could swap
        the nodes visited, but not their parents (which could be different at
        the root level), leading to a node with itself as the putative parent.

    Solution:
        When swaping the nodes, swap the parents.

Improvements:
    Added numerous assertion checks for the auto_sequence_partition commands and
    other related commands.

Bugfix:
    Symptom:
        Tests for file 10.fas fail in the test machine vamsi.
    Problem:
        The prepend and tail costs arrays are allocated for type SEQT when they
        should be for site int as they hold a cost. This causes a segfault when
        we attempt to copy the contents of the cost matrix.
    Solution:
        Allocate the proper size.

Bugfix:
    Symptom:
        auto-static-approx may fail under amd-64 architectures.

    Problem:
        We use a Bigarray with native-int representation in the OCaml side of
        the sequence unions offset, but a regular 32-bit int in the C side of the
        unions.

    Solution:
        We don't need 64 bits for the offsets, only 32 bits, so change the
        representation in the OCaml side to in32_elt.


New Configure Options:
    --enable-long-sequences
    --enable-large-alphabets

    See ./configure --help for more information.

Improvements:
    Updated the camlp4 based parsers and related error handling 
    to support camlp4 version 3.10.0.

Improvement:
    Diagnosis in xml formater for genome character is now available

Improvements:
    Added the gnu's config.guess and added the necessary tests in the
    src/configure.ac and src/configure scripts to use -fno-PIC when running in
    x86_64, as OCaml 3.10.0 is broken under the default options.

Bugfix:
    1. In poyCommand:
    Symptom: 
        The locus_breakpoint parameter did not work as described in documentation.

    Problem: 
        In poyCommand.ml, it was breakpoint instead locus_breakpoint
    Solution: 
        Change the breakpoint keyword to locus_breakpoint

Improvement:
    The single state for the multiple chromosome character is now available.

Improvements (and bugfix):
    Removed the duplicated specification of the upper and lowercase versions of
    the nucleotide and aminoacid alphabets. Instead, we use the new
    functionality to make a lexer that is not case sensitive.

    This fixes the previous commit which left the program in a non-executable
    state.

New Features:
    - Support for character names and labels in Hennig/Nona/TNT files (with the
      cname command).
    - Better support for command order and unknown commands in Hennig/Nona/TNT
      files.
    - report (diagnosis) and report (data) now include character labels and
      weighting schemes.
    - Support for real-valued weights for non-additive and additive characters.

Bugfix:
    
    Symptom:
        Parsing DNA sequence files with lower-case sequences fails.

    Problem:
        When using case insensitive parsers for alphabets (as molecular files
        do), the lexer fails to convert each input character to its uppercase
        representation.

    Solution:
        Add the appropriate Char.uppercase when needed.

Bugfix:
    Symptom:
        report (diagnosis) can fail with a Not_found error when Additive
        characters are present.

    Problem:
        The exception match has a typo.

    Solution:
        Correct the typo.

Bugfix:
    Symptom:
        Some times, reading a file can turn into an endless loop.

    Problem:
        When we read_line using our internal FileStream objects, the library
        fails to junk out some of the possible newline characters, while
        accepting them as end of line markers, therefore never passing one of
        the lines.

    Solution:
        Junk every valid class of newline character.

Improvements:
    Varius small improvements to the new Hennig/Nona/TNT parser.

    Added support to read Nexus files. Still need impmroved error messaging and
    a LOT of testing.

Improvements:
    Added support for implied alignments when using iterative pass. 

Improvements:
    Multiple simplifications to the configuration and compilation steps:

    - The default ./configure script will test for ncurses, and if not found,
      instead of failing will roll back to the readline interface.

    - When compiling for readline, POY will check for the availability of
      termcap, curses, or ncurses. These checks are non terminating.

    - A manual check for malloc.h will try to use /usr/include/malloc/malloc.h
      in case the failure occurs in Mac OS X.

    - make will automatically handle properly the parallel or non-parallel
      compilation steps, create dependencies. 

    - make install should work cleanly now.

Improvements:

    Added support for --program-prefix, --program-suffix, and
    --program-transform-name options in configure.

Bugfix:
    The size of the three dimensional and two dimensional matrices was
    insufficient and caused a buffer overflow. Although this could lead to a
    crash, it was not observed. Maybe other errors that we observed in the past
    where caused by this?

    The 3-dimensional matrix is again properly initialized depending on metric
    settings and alphabet specification, just as the two dimensional matrix is.

Improvements:
    When converting from the POY to the ukkCommon sequence representation, don't
    check for base value equality, but rather bitset intersection. In this way
    we ensure proper filtering of sets of sequences into a single sequence.

Bugfix:

    When initializing the three dimensional matrix, handle properly the
    non-metric cases by sticking to the union of sets of alphabet elements when
    calculating the median, as opposed to any possible combination.

Improvements:

    Use the three dimensional matrix to pick the median of the 3-dimensional
    readjustement (used in interative pass).

Bugfix:
    Symptom:
        Starting poy in 64 bit architectures fails with an assertion failure.

    Problem:
        The three dimensional cost matrix is initialized with max_int, which in
        a 64 bit architecture is larger than our C representation (32 bit
        integer), which therefore has a negative number, yielding a set of
        uninitialized matrix medians.

    Solution:
        Use the Int32.max_int number to initialize the matrix.

Bugfix:
    Symptom:
        32 bit linux execution fails with an Assertion failure in
        Cost_matrix.
    Problem:
        A previous bugfix for 64 bit environments produced a 32 
        bit integer in 32 bit environments, when OCaml can handle 
        integers with at most 31 bits.
    Solution:
        Override max_int in Cost_matrix.ml so that it's always 2^30 - 1.

New Command:
    report -> supports -> jackknife[:(individual | consensus)]
    report -> graphsupports -> jackknife[:(individual | consensus)]
    report -> supports -> bootstrap[:(individual | consensus)]
    report -> graphsupports -> bootstrap[:(individual | consensus)]

    See the program documentation for further information.


Bugfix:
    Symptom:
        help () does not show all the help.

    Problem:
        Commenting latex breaks our latex parser! 

    Workaround:
        Don't comment the all_commands.tex file! 

BugFixed:
    Problem: User-defined parameters were not passed to compute 
             medians for chromosome chracters when constructing
             implied alignments.

    Solution: Pass the user-defined parameters properly

Improvement:
    Add the attribute "definite" to the xml output
    for the seq and  chromosome characters. If there
    is no change between ancestor and descendant,  
    definite=false, otherwise definite=true

Improvements:
    When reading dpread files, POY doesn't recognize when the input matrices are
    really non-additive matrices. This causes a tremendous overhead in time and
    space for the computations. I have added a function to check if the input
    matrix is really a non-additive one.

Bugfix:
    Added compilation rules for the hennig and nexus lexers and parsers.

Bugfix:
    Symptom:
        Reading prealigned files could fail with a Not_found error (Frederic
        Legendre).

    Problem:
        If a taxon is missing from the input file, the program has no case to
        handle gracefully the missing data.

    Solution:
        Ignore the missing taxon and continue with the next character.


Improvements:
    Better error message when the OCaml version dependency is not filled.

Bugfix:
    Symptom:
        When converting sequences from chromosomal to regular sequence
        characters, the transformation cost matrix assigned to them is rolled
        back to the default.

    Problem:
        The tcm was never passed but always assumed. Therefore, the default was
        assigned.

    Solution:
        This problem goes away once the defaults are removed from Data.d.

Improvements:
    Added support for the Unaligned block of Nexus files.

Improvements:
    Change the default value of rearranged_len from 1000 to 100
    so that we can cover smaller rearrangements

Bugfix:
    Symptom:
        Setting the margin on files that have not been opened yet has no effect
        in the format of the file.

    Problem:
        We ignore the settings if there is no formatter assigned to a particular
        filename. 


    Solution:
        If there is no file assigned to a name, create it, and assign it's
        formatting properties immediately.

Improvements:
    Simplified the xml document formatting.

Bugfix:
    Symptom:    
        Reading certain filetypes could make POY crash.

    Problem:
        We don't verify the correctness of the boundaries of the character 
        codes when when using ranges.

    Solution:
        Check that we don't pass the number of actual characters and taxa 
        being included in a matrix.

Improvements:
    Added support for libxslt and postprocessing of xml output using an xslt
    template.

New Configuration Options:
    --enable-xslt
    --with-xslt-config=program

    See ./configure --help for more information

New Commands:
    report -> xslt:(STRING, STRING). The first string is the filename of the
    output, the second the stylesheet to be applied to generate it.

Bugfix:
    Symptom:
        report (diagnosis) can fail sometimes with a Invalid_code(_) exception.

    Problem:
        We assume that if no alphabet is assigned to a set of states, they are
        integer codes, and each code matches it's string representation.
        However, we start assigning codes from 1, when the input might start
        from 0.

    Solution:
        Assign codes starting in 0.

Bug Fixed:
    Symptom: 
        The Tcm transform did not go into chromosome data.
    Problem: 
        Forgot to pass tcm to chromosome characters. The 
        default tcm was used.

    Solution: 
        Pass the transformed tcm to chromosome characters.

Bugfix:
    Symptom:
        Custom alphabets of 65 elements cause a segmentation fault in 32 bit
        architectures.

    Problem:
        1. The size of the cm matrix produces an allocation of size 0 which might
           not be caught in some architectures.
        2. We allocate cost matrices biger than required (twice as much as needed).

    Solution:   
        Check for a positive allocation size, otherwise fail with a meaningful
        error message.
        Allocate a tighter cost matrix.

New Feature:
    The cost matrix for custom alphabets is not obligatory anymore. Instead, if
    such matrix is empty, we create a default matrix for the specified alphabet.

Bugfix:
    Symptom:
        During tree fusing, POY can stop the procedure with an assertion failure
        in line 1368 (Kurt M. Pickett).

    Problem:
        During a filtering step, we inconsistenly pick the adjusted and
        unadjusted costs, causing a theoretically impossible situation.

    Solution:
        Always pick the adjusted cost.

Bugfix:
    Symptom:
        Reading tread commands with comments from Hennig86/Nona files fails.

    Problem:
        The lexer did not have rules to ignore the comment.

    Solution:
        Add the required rules.

Improvements:
    Updated the diagnosis to properly handle iterative pass. The process caused
    several changes in the interface of the functions related.

New Features:
    Added a stylesheet to produce a graphical tree output from the xml output.

Improvments:
    Factored out functions from the original svgtree.xsl in two components,
    printtree.xsl and branchlength.xsl to handle the different portions of the
    tree pretty printing transformations.

Bug fixed:
    Symptom: 
        The cost of the tree after tranforming to static approximation for
        chromosome and annotated chromosomes are higher then the cost before
        transforming
    Problem: 
        The assignment of single sequence for the root for chromosome characters
        are not correct. 

    Solution: 
        Assign the correct single states for the root of chromsome chracters

Bug fixed:

    Symptom: 
        Transform to static approximation of breakinv chracters when orientation=true
        cause the tree cost equal to zero. 

    Problem: 
        The negative gap (~-) problem. The cost between all states and negative gap 
        is zero.


    Solution: 
        Fix such that the cost between all states and negative gap is the same
        as positive gap

Improvements:

    Added coloring, branch lengths (the number), and optional parameters for the
    stylesheets, like width of the strokes, color of the default strokes, among
    others.

Bugfix:
    Symptom:
        report (phastwinclad) does not change the character type of all the
        characters.

    Problem:
        We recode the character type of those characters that are to be used in
        an analysis. However, we print all the characters, even those that have
        not relevance for the analysis itself.

    Solution:
        Recode every character, and don't limit the functions to those listed in
        Data.d.<character_type>

Bug fixed:
    Symptom:
        When diagnose the chromosome characters, the chromosome map between
        handle and its parent is not correct.

    Problem: 
        We diagnose the map between handle and its child.

    Solution: 
        Diagnose the map between the handle and its parent.

Bug fix:
    Symptom: crashed when creating implied alignment

    Problem: This script intended to test annotated chromosome, however, 
    the read command specifies the data type as chromosome.

    Solution: specify the data type as annotated in the read command

Improvements:
    Improved the character transformation for static homology characters under
    affine gap costs, separating characters in the individual substitutions, and
    the blocks of indels. Their state names match those indels occuring in the
    sequences.

Bugfix:
    Symptom:
        The maximum cost of the single assignment (and potentially preliminary
        and final too), can be lower than the minimum cost.

    Problem: 
        The maximum distance function does not add the gap opening cost when
        comparing a pair of aligned sequences.

    Solution:
        Add rules to include the gap opening cost.

Bug fixed:
    Symptom: Crashed when assign single states for trees with approx=true

    Problem: The mean sequence between chromosomes A and B was assigned
             by the true mean sequence between them, not A or B as requested
             be approx=true

    Solution: Asssign A for the mean sequence between A and B when approx=true
             
Bug fixed:
    Symptom: Crashed when assign single states from the genome character
    Problem: Wrongly adding the missing loci when creating the map 
             between two chromosomes

    Solution: Fix this mistake
    

------------------------------------------------------------------------
r2160 | andres | 2007-08-29 16:51:18 -0400 (Wed, 29 Aug 2007) | 4 lines

Improvements:
    Improved proper handling of max distance when one of the sequences is
    missing data.

Improvements:
    Completely dropped the gcc version requirements from the configuration
    scripts and program documentation.

Bugfix:
    Symptom:
        The maximum distance for the single sequence assignment is greater than
        expected.

    Problem:
        The default cost being assigned to the gap opening when using linear gap
        costs is 1, not 0. As no alignment is performed, we don't pick different
        functions for the maximum distance between aligned sequences, but jusst
        calculate the distance using the value stored for gap opening. The
        stored value is not 0 under atomic costs, but 1, causing the disparity.

    Solution:
        Make the default value 0 for Linear cost matrices.
Bugfix:
    Symptom:
        read (prealigned:("file", tcm:(1, x))) does not match the cost of the tree
        when the alignment comes from the implied alignment for the same tree ,
        and the same tcm, when x <> 1.
    Problem:
        The encoding functions recognize 0 as the gap representation, as this is
        the implied alignment representation. However, we do pass the actual
        code for the gap in the sequence, causing an extra character where the
        encoding needs inapplicable data.
    Solution:
        Catch the gap case and conver it to a 0 before asking the encoder to
        make the proper character code.

Bugfix:
    Symptom:
        After reading prealigned sequences with tcm:(1, x) where x <> 1, the gap
        representation is assigned a non-valid alphabet set (the same as the
        alphabet itself!. 

    Problem:
        We remove the alphabet of each character and use the general alphabet of
        the sequence for the encoding. 

    Solution:
        Use a per-character alphabet (as passed from the encoder function),
        instead of the general sequence character alphabet.

Bugfix:
    Symptom:
        Reporting phastwinclad produces a file with overly too many newlines (to
        the point where it becomes an illegal file).

    Problem:
        We don't turn off the pretty printer and attempt to change the margin by
        setting it to 0, which effectively doesn't change the margin in OCaml
        3.10.0.

    Solution:   
        Set the margin to a large value, and make the newlines hard newlines
        instead of formatter hints.

Bugfix:

    Symptom:
        When multiple fragments have affine gap costs, the static approximation
        does not properly add the blocks generated by each fragment.

    Problem:
        We don't fold over the list of all the sets of blocks, but only
        operate in the first element of the list.

    Solution:
        Fold over the list to deal with every set of blocks.

Bugfix:
    Symptom:
        report ("x", phastwinclad) can fail with a segmentation fault.

    Problem:
        The Format module can have a stack overflow for the large number of
        columns that we accept in files for this kind of output (100000).

    Solution:
        As in a toilet: don't forget to flush, but be antiecological: flush
        often.

Improvements:
    Added a configuration-time option to verify the cost of all pairwise
    alignments (--enable-cost-verification). See the help for further
    information. This simplifies the check of errors reported by tests when the
    cost of a tree does not match the expected cost, as we might be changing
    slightly the overall tree cost estimation, and there might be no error in reality.

    This change required the modification of the configuration scripts and
    Makefiles. seqCS.ml now needs to be preprecessed by camlp4 to handle the
    compile time option properly.

Documentation Update:
    - Improved the description of the command 'use' and
      supplied it with examples
    - Corrected minor formatting inconsistencies

Algorithm changed:
    Change chromosome characters such that it is correct
    for creating the implied alignment using single state

Documentation update:
    - Added missing examples and corrected existing examples
      pertaining to the arguments 'gap_opening', 'weight',
      'weightfactor', and 'fixedstates' of the command
      'transform'.

Documentation update:
    - Improved descriptions of multiple arguments that were added
      between builds 1852 and 2093

Bugfix:
    Symptom:
        swap (trees:x) may finish with no trees in memory.

    Problem:
        The subset of trees selected at the end of the search contains one less
        than the actual number of trees stored in the queue. If there are more
        than one trees on it, the bug is unnoticeable, but if only one, then no
        trees are returned.

    Solution:
        Fix the subarray size.

Improvements:
    Changed the color and welcome message to match the GUI icon and the new status
    of the binaries (Release Candidate).



CHANGES BETWEEN BUILD 1908 AND 1983

IMPROVEMENTS AND NEW FEATURES:
    - Mac OS X has a Graphical User Interface.
    - Simplified the installation process in Mac OS X (just drag and drop).
    - Added support for reading prealigned sequences.
    - Added support to read CLUSTAL files.
    - The calculation of bremer supports using swap (visited:"file") and report
      (support:bremer:"file") was requiring the complete load on memory of the
      input file "file". However, those files tend to be quite large, making
      them useless. The new implementation reads the input file as a stream,
      processing one tree at a time, and never loading the whole file in memory.
      Although this method is slower, it makes usable any input file size.  
    - Added the configure scripts for easier compilation in Unix systems.
    - Added an html-output port. Instead of producing plain text, POY produces
      html pages.
    - Added the -f option to POY to avoid hanging in the absence of any further
      script to run (waiting for user input in a non-interactive kind of run).
      See poy --help for further information.
    - Added the alphabet specification in the character definition output (report
      (data)).
    - Turn on the approx parameter for chromosome characters
    - Added experimental support for iterative pass, BUT THIS IS NOT RECOMMENDED
      FOR USE. This is expected to be fully supported in the next release.


BUGFIXES:
    - Some searches could cause an endless loop (notably swap (all)).
    - transform (static_approx) fails for custom alphabets (Frederic Legendre).
    - Reading some custom alphabet matrices could cause a Not_found error (Megan
      Harrison).
    - The postscript output of consensus trees does not follow the standard tree
      order (depth, number of leaves) (Ward Wheeler).
    - Consensus trees appear in a different order than regular trees (the
      outgroup appears last) (Ward Wheeler).  Jackknife and Bootstrap support
      values are overly too low (even many zeroes) (Gonzalo Giribet).
    - Running transform (auto_sequence_partition) did not change the sequences
      although the input did not show any length variation (Gonzalo Giribet).
    - swap(exact) causes failwith "Get_active_ref_code in allDirChar.ml" even
      for sequence character.

NEW COMMANDS (SEE PROGRAM DOCUMENTATION):
    report -> seq_stats
    report -> compare
    transform -> prealigned
    read -> prealigned
    set ->cost_calculation

REMOVED COMMANDS
    swap -> exact


Changes between build 1902 and 1908

                                    BUGFIXES

Corrected a bug that affected the trees that POY prefers to test during a tree
build and local search when some sequences where missing. This bug biased
the searches depending on the ammount of missing data.

Deactivated the aproximate argument for chromosomal analyses.

Changes between build 1822 and 1902

                         IMPROVEMENTS AND NEW FEATURES

New Feature:
    The ncurses interface now supports command autocompletion. Just press tab
    and possible commands will be automatically completed.

Improvements (Parallel):
    The master process will not call the barrier until all other processes have
    reached it. In the meanwhile it will continue to print whatever messages are
    sent from the slaves. 

    I believe this is the cause of a strange crash in some scripts including
    swap (trajectory) or swap (visited) when running in parallel, but I am not
    enterely sure.

Improvements:
    Added the function to output a single state for each internal node
    for chromosome characters

Improvements:
    Added the function to output a single state for each internal nodes
    for chromosome chracters

User Interface Flat:
    Added support for readline. This adds history, filename completion, line
    edition, and a command prompt to the flat interface. It makes it very
    powerful indeed.

User Interface Ncurses:
    Added the much needed filename autocompletion!. For example, if your current
    directory has the files chel.aln, chel.ss, and chel.tree, typing:
    read ("chel.<TAB>  
    will complete to chel.aln
    pressing tab again will complete to chel.ss
    pressing tab again will complete to chel.tree
    pressing tab agina will complete to chel.
    pressing tab again will repeat the cycle.

    It works for all strings. 

Makefile Changes:
    The readline library is now required by POY.

Improvements:
    After transform (fixedstates), assign the original name of the sequence
    character to the resulting character, instead of the temporary filename.

New Commands:
    swap -> visited
    report -> supports -> bremer [: STRING] (bremer existed in supports, 
    but with no optional argument).

    See the manual for further information.
New Features:
    report (phastwinclad) now includes Sankoff characters if the dataset has
    them. The resulting file is a dpread file as defined in the POY
    documentation.

    Improvements:
        The phastwinclad file report will respect the order of the bases in
        regular sequences. In this way, it is possible to map each base in an
        implied alignment to the corresponding bases (or combination of
        characters), after the static approximation transformation (provided the
        keep option is used in static_approx).

    Improvements:
        The static_approximation of extension gap costs does take into
        consideration the characteristics of this gap cost regime. Although the
        cost of the trees changes, we limit as much as possible the space
        distortion by separating characters for gap openings, gap extension, and
        substitutions.

New Features:
    New Argment:
        build -> all
        See the documentation for further information.

New Commands:
    swap -> visited
    report -> supports -> bremer [: STRING] (bremer existed in supports, 
    but with no optional argument).

    See the manual for further information.

                                    BUGFIXES

Bugfix:
    Symptom:
        During some searches POY enters an endless loop (Johan Anas).

    Problem:
        The search manager of the alternate swap strategy is not propely cloned
        when going from tbr to spr.

    Solution:
        Clone the search manager.

Bugfix:
    Symptom:
        Starting poy with the ncurses interface in a white terminal can have the
        background scrambled. This is known to happen at least in Mac OS X 
        Terminal.app.

    Problem: No problem. Apparently ncurses does not update the whole window.

    Solution: Simply redraw the nucrses windwos again after launching POY.

Bugfix:

    Symptom:
        Some pairwise alignments using extension gap have an incorrect (lower) cost
        (Kevin Liu).

    Problem:
        The initialization of the first cell of each row had some small
        invariants broken in some branches of the Ukkonnen barriers, leaving the
        calculated cost incorrect.

    Solution:
        Update the invariants of the Ukkonnen barrier - based alignments to
        match that of the full plane alignments (which is correct).

Bugfix:

    Symptom:
        Dragging and dropping filenames with spaces does not work in Mac OS X
        (Julian Faivovich).

    Problem:
        Mac OS X escapes the spaces when dragging and dropping them to the
        terminal, while other OSes don't. The escape then is escaped internally
        by POY producing a double \ which yields and unexistent path.

    Solution:
        Replace escaped spaces with regular spaces in every path.
Bugfix:
    Symptom:
        transform (fixed_states) keep the old character set.

    Problem:
        The characters selected for the transform are never removed.

    Solution:
        Filter the necessary characters from the data.

Bugfix:
    Symptom:
        Diagnosis of mixed character types causes a crash.

    Problem:
        Certain characters are filtered out from a single assingment, causing
        internal inconsistencies, instead of being assigned themselves.

    Solution:
        Do not filter any character for the single assignment.

Bugfix:
    Symptom:
        Using extended alphabets can cause POY to crash when producing an
        implied alignment (Frederique Legendre).

    Problem:
        The implied alignment functions in POY assumed nucleotide alphabets in
        many little details.

    Solution:
        Generalize the functions to deal with them properly.

Bugfix:
    Symptom:
        Using extended alphabets can cause POY to crash during a search if the
        cost regime is modified (eg. transform (tcm:(1,1))) (Ward Wheeler,
        Frederique Legrenge).

        Using transform (static_approx) of extended alphabets produces bogus
        tree costs (even negative ones!). (Ward Wheeler).

    Problem:
        The tcm for all aphabets had size 5 (assuming a nucleotide size). 

    Solution:
        Generalize properly the tcm size after a transform.
Bugfix:
    Symptom:
        Sankoff characters are not printed in the report (data) command.

    Problem:
        The contents of Saknoff characters was not processed in the to_formatter
        function.

    Solution:
        Add the required processor.

Bugfix:
    Symptom:
        transform (static_approx) for cost matrices that involve Sankoff
        characters yields trees overly too short (Ward Wheeler).

    Problem:
        Gaps where being encoded as missing data.

    Solution:
        Code gaps as the fifth state they are.

Bugfix:
    Symptom:
        When reading dpread files, a costs command does not properly handle
        ranges of characters. For instance, costs 0.25 changes the cost of
        characters 0 and 25 instead of characters 0 to 25.

    Problem:
        The dot is wrongly replaced with a space, being therefore interpreted as
        a list of characters instead of a range.

    Solution:
        Remove the regex replacement.

Bugfix:
    Symptom:
    
        The application of format options in a file output is not performed if the
        file's channel has already been opened.

    Problem:
        When the channel exists, there is no formatter call.

    Solution:
        Add the required function call.

--------------------------------------------------------------------------------

Changes between build 1724 and 1822.

Bugfix:
    
    Symptom:
        Some processes appear to take too long (Torsten Dikow)
        Searching could continue with an endless loop.

    Problem:
        The threshold selection functions in the queue managers did not verify
        the cost of a tree before adding it to the queue. This caused an
        unlikely endless loop when swap (trees:1), but if trees > 1 or threshold
        > 0.0, the likelihood is much greater.

    Solution:
        Verify the cost before filtering out.


Bugfix:
    
    Symptom:
        Including trajectory in the swap argument causes a Not_found exception
        raised (Torsten Dikow).

    Problem:
        After transforming a tree when using static homology only characters,
        the codes of the internal vertices is not valid anymore. But this
        information is not required for trajectory reports.

    Solution:
        Catch the exception and return the empty string then.

New Commands:
    build (0) 
    build (of_file:"filename")
    build ("filename) 
    are supported now. See the documentation for further details.

Improvements:
    Improved the performance of the support calculations.

Improvements: 

    The search performance has been improved if only static homology characters
    are loaded. This will also work if the change comes from a (possibly
    temporary) transform (for example transform (static_approx)).

New Feature:

    Added the -no-output-xml option to turn off all output.xml generation. 

    The output.xml file will not be generated by processes other than the master
    in a parallel run. This is causing possible crashes when running in
    parallel.

Bugfix:

    Symptom:
        Reading trees from a hennig file makes them "sticky", loading them once
        after reading any other file, although a select (best:0) has already
        been requested eliminating them (Paola Pedraza).

    Problem:
        The trees are stored temporarily in the Data.d structure, but they are
        not removed after loading. 

    Solution:
        Upon loading the trees from Data.d, make the list empty.

Bugfix:

    Symptom:

        Calculating costs with negative weights yield strange tree costs (Paola
        Pedraza).

    Problem:
        The adjusted tree lengths did not include the weight of the sequences in
        in the adjustement, causing the lengths to be positive, making a
        substraction the addition of negative values.
        The incorrect function was Node.total_cost_of_type

    Solution:
        Multiply the cost of each type by the corresponding weight.

Bugfix:
    Symptom:
        POY crashes during bootstrap if using static_approx (Louise Crowley, Ward
        Wheeler).

    Problem:
        An incorrect filtering in the interior vertices caused an incorrect set
        of homologous characters.

    Solution:
        The previous implementation used a per-node filtering because loading
        nodes was too slow. We have replaced it now with an in Data.d
        resampling, and loading fresh nodes. There is no need to repeat complex
        code in the Nodes.

Improvements:

    The timed_printout sampler now is called more often, to achieve a
    more accurate sampling rate.

Bugfix:

    The timedprint did not update the contents of the timer, effectively
    triggering the print functions every time it was called after the first n
    seconds. 

    This has been corrected now.

Improvements:

    Increased the checking speed of the timedprint.

Improvements:

    Added support for proper error message printing and exit code (1), when the
    program finishes with an uncaught error.

Bugfix:
    The thread identifier of Concurrent was in reverse order, making it
    impossible to find it's corresponding `Store label during linnearization.

Improvements:
    The behavior of the swap (timout:n) command has been changed. Now the
    command will timeout argument is used in a per-trajectory basis, not in a
    per-search basis. In this way, the behaviour of a script is more
    predictable, and it's easier to use a timeout argument inside other commands
    such as perturb or fuse.

    For example, if swap (timeout:10) is used, each tree will be swaped for at
    most 10 seconds, and returned. Therefore, if there are 10 trees, at most 100
    seconds will be spent on the search. If used with the recover argument, the
    user will be guaranteed to have in memory the best tree that could be found
    with a 10 second search performed on each of the input trees.

Bugfix:
    Multiple bugfixes in the affine gap cost calculation backtrace and
    pairwise distance function for sets of sequences.

New Feature:
    Supports the calculation of affine gap cost regimes where the TCM itself
    is non-metric (Kevin Liu).

Bugfix:

    Symptom: 
        The calculation of the length of a tree under affine gap cost model is
        incorrect (Kevin Liu).

    Problem:
        The selection of an affine gap cost model requires two consecutive
        commands. First, the desired substitution, gap extension costs are set
        using the tcm argument of transform, and then the gap opening cost is
        set. 

        POY implements a correction of the pairwise distance for affine costs, 
        but the correction was incomplete even when the transformation cost
        matrix itself is not metric, and there where still some holes in the
        metric case.

    Solution:
        Whenever a set of medians could have either a block of gaps, or a block
        of bases, and a new alignment could break it in two sections, add to the
        total cost the gap opening paramenter (alwasy). In the same way, if the
        cost between an a pair of aligned sequences includes a gap in exactly one 
        of them in their respective sets, add the gap opening cost.

Bugfix:

    Symptom:
        Attempting to do tree fusing when only one (or no) trees are in memory
        cancels the script (Ward Wheeler, Torsten Dikow).

    Problem:
        The error raised by the fusing function passes uncaught.

    Solution:
        Catch the error and continue the regular execution of the rest of the
        script.

Bugfix:
    Symptoms:
        Some times the order of execution is different from the input script
        (although the execution itself is still correct).

    Problem:
        A case in the analyzer didn't have the necessary child sorting function.

    Solution:
        Add the children sorting function to the case that missed it.


Bugfix:
    Symptom:
        Scripts that run sevaral searches using different cost regimes do not
        produce correct output, but rather repeat the results of one of the
        searches, or do not produce output at all (Joseph Spagna, Christian
        Kehlmaier, Ilya Temkin, Paola Pedraza).

        A simplified example of such behavior is the script 
            read ("a") build (1) transform (tcm:(1,1))
        which terminates in the interactive state of the POY session with no
        trees in memory.

    Problem:
        Two related problems are occurring: although POY analyzes the data
        dependencies of the script correctly, it is storing the global state of
        the program when selecting a different execution path in a script.
        Therefore, if a command (like transform (tcm:(1,1)) only depends on the
        data as produced after read ("a"), and affects both data and trees, the
        analyzer has to properly select the correct source for each component,
        instead of using the global state of the search as produced right after
        the read command.

        Similarly, although reporting sets a file output constraint, this
        constraint is immediately fulfilled at the time of execution of the
        command if other commands outputting to the same file have already been
        executed. For this reason, the execution of the reports should not be
        delayed due to this constraint, but rather ensured to occur _after_
        other reports to the same file occur. This can be guaranteed by simply
        ensuring the correct order of execution as input by the user, which is
        already done in the current code.

    Solution:
        Add a parameter in the Store, Set, and Discard constructors of the POY
        scripting to specify the class of information (Data, Trees, Jackknife,
        Bootstrap, or Bremer) to be stored, and ensure that the appropriate
        information is stored when more than one execution path is possible.
        This solution has been implemented in the last two commits to the source
        repository.

        For the report problem, simply drop the filename constraint, and only
        include it in the field that specifies what components are affected by a
        command. This solution is implemented in this commit, to finish solving
        the overall problem.

New Command:

    report -> timer 
        See the user documentation for further information.


Improvements:

    Added functionality to recover a single median assignment to each vertex for
    tree cost verification. 

New Feature:

    Implied alignment is now available for chromosome character
    (but not yet annotated chromosome and breakinv chracters)


New Feature:

    If the diagnosis or the data are reported to an XML file (a file with
    extension xml), then the output is not formatted as tables as usual, but as
    an XML dump. Currently the format of this XML file is not very well
    established though and will change in the future.