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Andres Varon
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[svn] Initial branch of version 4.1 development.
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‎AUTHORS

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Andr�s Var�n <[email protected]>
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Le Sy Vinh <[email protected]>
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Illya Bomash
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Ward Wheeler <[email protected]>

‎COPYING

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‎INSTALL

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In order to compile POY, the minimal requirements are:
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- Objective Caml version 3.10.0, which can be found in
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http://www.ocaml.org.
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- An ISO 99 C compiler.
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- The GNU Make toolbox (version 3.80).
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- Readline or ncurses
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To compile the program, first modify the relevant paths and options in config
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(there is a brief description on each group of options or you can see the
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program's documentation), and then simply:
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./configure
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make
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make install
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The last command should probably be run as superuser. Check the configuration
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options with ./configure --help.
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Enjoy!

‎LICENSE

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POY 4.0 Beta. A phylogenetic analysis program using Dynamic Homologies.
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Copyright (C) 2007 Andr�s Var�n, Le Sy Vinh, Illya Bomash, Ward Wheeler,
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and the American Museum of Natural History.
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This program is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation; either version 2 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program; if not, write to the Free Software
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Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301
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USA

‎Makefile.in

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# $Id: Makefile 1485 2007-01-04 23:08:52Z andres $
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# Compilers
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SHELL = /bin/sh
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VPATH = @srcdir@
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subdirs=@subdirs@
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top_srcdir = @top_srcdir@
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srcdir = @srcdir@
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prefix = @prefix@
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exec_prefix = @exec_prefix@
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bindir = $(exec_prefix)/bin
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infodir = $(prefix)/info
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libdir = $(prefix)/lib/gnudl
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mandir = $(prefix)/man/man1
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CC = @CC@
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CPPFLAGS = @CPPFLAGS@
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CFLAGS = $(CPPFLAGS) @CFLAGS@
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LDFLAGS = @LDFLAGS@
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LIBS = @LIBS@
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INSTALL = @INSTALL@
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USEPARALLEL := @USEPARALLEL@
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SUBDIRS = ocamlmpi src doc
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all:
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ifeq ($(USEPARALLEL), true)
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cd ocamlmpi; $(MAKE)
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$(MAKE) depend
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cd ../src/; $(MAKE) poy
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else
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$(MAKE) depend
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cd ./src/; $(MAKE) poy
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endif
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.PHONY: subdirs $(SUBDIRS) clean driver install
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subdirs: $(SUBDIRS)
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transform = @program_transform_name@
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install:
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$(INSTALL) ./src/poy $(bindir)/`echo poy | sed -e '$(transform)'`
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uninstall:
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rm -f $(bindir)/`echo poy | sed '$(transform)'`
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MAKEOCAMLMPI :=
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ifeq ($(USEPARALLEL), true)
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MAKEOCAMLMPI := ocamlmpi
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endif
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binaries: mpoy-single mpoy-dual
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mac_panther:
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cp -f config myconfig
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cp -f config.panther config
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$(MAKE) clean; $(MAKE) depend; $(MAKE) mpoy.opt
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cp -f myconfig config
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cp src/mpoy.opt ./panther/poy
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mac_ppc:
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cp -f config myconfig
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cp -f config.ppc_seq config
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$(MAKE) clean; $(MAKE) depend; $(MAKE) mpoy.opt
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cp -f myconfig config
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mac_ppc_parallel_flat:
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cp -f config myconfig
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cp -f config.ppc_par_ncurses config
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$(MAKE) ocamlmpi
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$(MAKE) clean; $(MAKE) depend; $(MAKE) mpoy.opt
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cp -f myconfig config
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mac_ppc_parallel_ncurses:
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cp -f config myconfig
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cp -f config.ppc_par config
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$(MAKE) ocamlmpi
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$(MAKE) clean; $(MAKE) depend; $(MAKE) mpoy.opt
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cp -f myconfig config
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mac_ppc_parallel:
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$(MAKE) mac_ppc_parallel_ncurses
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cp src/mpoy.opt ./universal_parallel/mppoy_ppc
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$(MAKE) mac_ppc_parallel_flat
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cp src/mpoy.opt ./universal_parallel/ppoy_ppc
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mac_intel:
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cp -f config myconfig
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cp -f config.intel_seq config
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$(MAKE) clean; $(MAKE) depend; $(MAKE) mpoy.opt
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cp -f myconfig config
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mac_intel_parallel_flat:
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cp -f config myconfig
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cp -f config.intel_par config
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$(MAKE) ocamlmpi
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$(MAKE) clean; $(MAKE) depend; $(MAKE) mpoy.opt
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cp -f myconfig config
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mac_intel_parallel_ncurses:
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cp -f config myconfig
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cp -f config.intel_par_ncurses config
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$(MAKE) ocamlmpi
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$(MAKE) clean; $(MAKE) depend; $(MAKE) mpoy.opt
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cp -f myconfig config
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mac_intel_parallel:
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$(MAKE) mac_intel_parallel_ncurses
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cp src/mpoy.opt ./universal_parallel/mppoy_intel
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$(MAKE) mac_intel_parallel_flat
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cp src/mpoy.opt ./universal_parallel/ppoy_intel
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mac_universal:
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$(MAKE) mac_intel
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cp -f ./src/mpoy.opt ./universal_sequential//poy_intel
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$(MAKE) mac_ppc
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cp -f ./src/mpoy.opt ./universal_sequential/poy_ppc
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lipo -create ./universal_sequential/poy_ppc ./universal_sequential/poy_intel -output ./universal_sequential/poy
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mac_universal_parallel:
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$(MAKE) mac_intel_parallel
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$(MAKE) mac_ppc_parallel
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lipo -create ./universal_parallel/ppoy_ppc ./universal_parallel/ppoy_intel -output ./universal_parallel/ppoy
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lipo -create ./universal_parallel/mppoy_ppc ./universal_parallel/mppoy_intel -output ./universal_parallel/mppoy
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mac_all:
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$(MAKE) mac_panther
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$(MAKE) mac_universal_parallel
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$(MAKE) mac_universal
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mpoy-single: $(MAKEOCAMLMPI)
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./set-config.pl --ncurses --no-parallel
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cd src; $(MAKE) clean; $(MAKE) .depend; $(MAKE) mpoy.opt
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mv src/mpoy.opt $@
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mpoy-dual: $(MAKEOCAMLMPI)
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./set-config.pl --no-ncurses --parallel
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cd src; $(MAKE) clean; $(MAKE) .depend; $(MAKE) mpoy.opt
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mv src/mpoy.opt $@
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poy:
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cd src; \
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$(MAKE) $@
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mpoy: $(MAKEOCAMLMPI)
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cd src; \
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$(MAKE) $@
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mpoy_console: $(MAKEOCAMLMPI)
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cd src; \
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$(MAKE) $@
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depend:
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cd src; \
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$(MAKE) $@
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$(SUBDIRS):
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$(MAKE) -C $@
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clean_distros:
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rm -f universal_parallel/*
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rm -f universal_sequential/*
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rm -f panther/*
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clean:
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@for subs in $(SUBDIRS); do \
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cd $$subs; \
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$(MAKE) clean; \
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cd ..; \
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done

‎NEWS

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‎README

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README
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----------------------------------
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POY 4.0 Alpha
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-----------------------------------
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This is the Phylogenetic Analysis Program using Direct Optimization. See the
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user documentation in docs/commands.pdf (requires Latex2e).
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‎VERSION

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POY 4.0 Beta

‎config.win32

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# User Interface, set to flat if you want the flat interface (good for
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# clusters, or non interactive sessions), ncurses for the terminal based
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# interface, and gtk2 for the gtk2 based interface. ncurses and gtk2 require the
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# respective libraries; the later requires lablgtk2 installed in the system.
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export USEINTERFACE = ncurses
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# Parallel options
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# do you want to run in parallel?
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export USEPARALLEL = false
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# The processes do NOT share a hard drive? do you want the master to broadcast
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# the input files to each process? (requires a hard drive available for each processor)
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export USENOSHAREDHD = false
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export DESTDIRMPI = /usr/local/ocamlmpi
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export DESTDIRPOY = /usr/local/poy
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export MPIINCDIR = /usr/share/mpich/include
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export MPILIBDIR = /usr/share/mpich/lib
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export MPILNAME = mpich
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export USE_LARGE_ALPHABETS = false
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export USE_LONG_SEQUENCES = false
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# Compilers of choice
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export OCAML = ocaml
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export OCAMLC = ocamlc.opt
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export OCAMLOPT = ocamlopt.opt #-cc /opt/intel/cc/9.0/bin/icc -ccopt -i-static
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export OCAMLDEP = ocamldep
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export OCAMLTOP = ocamlmktop
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export OCAMLMKLIB = ocamlmklib
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export OCAMLYACC = ocamlyacc
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export OCAMLLEX = ocamllex
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export INCLUDE = `ocamlc -where`
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export DEPEND = .depend
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# Compilation flags
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export FLAGS = -c\ -Wall
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export MKLIBOPT =
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# The following are the recommended flags, depending on the class of processor.
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# If you want to compile with USEPARALLEL = true, make sure you add -cc mpicc in
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# the CCOPT of your choice.
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# Intel Processors
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CCOPT := -ccopt -O3 -ccopt -msse2 -ccopt -mmmx -ccopt -march=pentium4
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# PowerPC G4 and G5
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#export CCOPT = -ccopt -O3 -ccopt -maltivec -ccopt -mpim-altivec -ccopt -I/usr/include/malloc/ -ccopt -mcpu=G4 -ccopt -g
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# graphical output options: ocaml,tk
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# non-graphical output: none
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export USEGRAPHICS = none
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#If compiling for windows, set the following to true and use the following
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#compilation flags.
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export USEWIN32 = true
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#export CCOPT = -ccopt -mno-cygwin -ccopt -O3 $(MYARCH_CCOPT)

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