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newick-tools: a novel software for simulating and processing phylogenetic trees

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Introduction

The aim of this project is to implement a proper, multifunctional newick manipulation toolkit called newick-tools. The toolkit should:

  • correctly parse newick files, both binary rooted and binary unrooted.
  • parse n-ary newick files and allow collapsing into binary rooted/unrooted.
  • parse the newick extended format
  • create new topologies from existing one by pruning taxa, or inducing subtrees.
  • generate topologies
  • list taxa, or taxa of specific subtrees
  • visualize the tree in terminal (ASCII), vector formats such as SVG and EPS, and raster format such as PNG.
  • compare topologies
  • root trees given outgroup taxon or outgroup subtree
  • locate repeated substructures (subtree repeats)
  • display tree info (rooting,number of taxa, max branch length, average branch length etc)
  • generate a consensus tree from a collection of trees.
  • perform all above functions on files that contain more than one tree, e.g. induce the subtrees of specific taxa in a collection of trees.

Compilation instructions

Currently, newick-tools requires that GNU Bison and Flex are installed on the target system. On a Debian-based Linux system, the two packages can be installed using the command

apt-get install flex bison

newick-tools also requires that a GNU system is available as it uses several functions (e.g. asprintf) which are not present in the POSIX standard. This, however may change in the future such that the code is more portable.

newick-tools can be compiled using the included Makefile:

make

Command-line options

General options:

  • --help
  • --version
  • --quiet
  • --precision
  • --seed

Options for binary trees:

  • --lca_left
  • --lca_right
  • --identical
  • --extract_ltips
  • --extract_rtips
  • --svg
  • --induce_subtree
  • --subtree_short
  • --svg_legend_ratio

Options for unrooted trees:

  • --root

Options for all tree types:

  • --extract_tips
  • --prune_tips
  • --prune_random
  • --tree_show
  • --make_binary
  • --info

Options for visualization:

  • --svg_width
  • --svg_fontsize
  • --svg_tipspacing
  • --svg_legend_ratio
  • --svg_nolegend
  • --svg_marginleft
  • --svg_marginright
  • --svg_margintop
  • --svg_marginbottom
  • --svg_inner_radius

Input and output options:

  • --tree_file
  • --output_file

License and third party licenses

The code is currently licensed under the GNU Affero General Public License version 3.

Code

File           | Description

-------------------|---------------- newick-tools.c | Main file handling command-line parameters and executing corresponding parts. Makefile | Makefile. lex_rtree.l | Lexical analyzer parsing newick rooted trees. lex_utree.l | Lexical analyzer parsing newick unrooted trees. lex_ntree.l | Lexical analyzer parsing newick n-ary trees. util.c | Various common utility functions. arch.c | Architecture specific code (Mac/Linux). rtree.c | Rooted tree manipulation functions. utree.c | Unrooted tree manipulation functions. ntree.c | n-ary tree manipulation functions. parse_rtree.y | Functions for parsing rooted trees in newick format. parse_utree.y | Functions for parsing unrooted trees in newick format. parse_ntree.y | Functions for parsing n-ary trees in newick format. lca_utree.c | Naive LCA computation in unrooted trees. lca_tips.c | Compute tips leading to an LCA node. svg.c | SVG output routines. prune.c | Methods for pruning taxa and inducing subtrees. info.c | Functions for showing various tree-related information.

Bugs

The source code in the master branch is thoroughly tested before commits. However, mistakes may happen. All bug reports are highly appreciated.

The team

  • Paschalia Kapli
  • Sarah Lutteropp
  • Tomáš Flouri