an algorithm to look for convergent signals in phylogenetic trees
Perl
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phyloconverge

README.md

phyloconverge

DESCRIPTION

phyloconverge has not been tested extensively and is being actively developed. Please use with caution. I appreciate hearing about your experience with the program.

phyloconverge is an algorithm to look for convergence based on a particular trait in a phylogenetic tree. The traits can be quantitative (e.g., size in centimeters or depth of observation) or can be categorical (e.g., associated with hydrothermal vents or not associated with hydrothermal vents).

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ALGORITHM

Essentially, the algorithm splits a tree (supplied in --treefile) in half (or as close to as half as possible) and compares the sum of attributes (supplied in --tabfile) of the clade with the highest sum of attributes to the maximum sum of attributes possible given the size of the clade and the taxa in the tree.

The priority for scoring is based on the evenness of the split, not the clade that encompasses the highest score for the trait.

AVAILABILITY

https://github.com/josephryan/phyloconverge (click the "Download ZIP" button at the bottom of the right column).

DEPENDENCIES

NOTE: python is called within perl to process the treefile

General system tools:

Additional libraries

INSTALLATION

To install phyloconverge and documentation, type the following:

perl Makefile.PL
make
make test
sudo make install

To install dendropy, depending on your system, you can probably use this command:

sudo pip install dendropy

RUN

phyloconverge --treefile=NEWICKTREEFILE --tabfile=TABFILE_W_ATTRIBUTES

EXAMPLE ANALYSES

phyloconverge --treefile=examples/converged.tre \
              --tabfile=examples/depths.txt

phyloconverge --treefile=examples/notconverged.tre \
              --tabfile=examples/depths.txt
              
converge_tree.py -t examples/notconverged.tre -d examples/depths.txt

To generate a table of results from many trees with one data file:

for T in Treefiles_*; do converge_tree.py -d datatable.txt -t "$T" >> AllResults.txt; done; 

DOCUMENTATION

VERY Extensive documentation is embedded inside of phyloconverge in POD format and can be viewed by running any of the following:

    phyloconverge --help
    perldoc phyloconverge
    man phyloconverge  # available after installation

COPYRIGHT AND LICENSE

Copyright (C) 2013 Joseph F. Ryan

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program in the file LICENSE. If not, see http://www.gnu.org/licenses/.