NAME

ppred-comp-test.pl - Compute compositional test based on ppred data

VERSION

version 0.180630

SYNOPSIS

    $ ppred-comp-test.pl test/for-ppred-comp.phy --phylip
        --sim-files=`ls test/ppred-*.phy`

This program implements the compositional test proposed by Blanquart and Lartillot (2008) based on simulated primary sequences. The compositional bias is computed for each sequence in the real alignment as well as in each of the simulated alignments. Two types of global biases (max and mean) are also computed. Z-scores are then computed to describe the ability of the evolutionary model to account for these biases. Any Z-score that is larger than 2.0 means that the model could not account for the compositional bias of the corresponding entity (single sequence or global).

USAGE

    ppred-comp-test.pl <infiles> --simfiles=<files>... [optional arguments]

REQUIRED ARGUMENTS

<infiles>

Path to input ALI files [repeatable argument]. If infiles are not in ALI but in PHYLIP format, use the --phylip option below.

--sim-files=<files>...

List of paths to simulated input files. These files are assumed to be in PHYLIP format as they result from PhyloBayes' ppred.

OPTIONAL ARGUMENTS

--from-scafos

Consider the input ALI file as generated by SCaFoS [default: no]. Currently, specifying this option results in turning all ambiguous and missing character states to gaps.

--del-const

Delete constant sites just as the -dc option of PhyloBayes [default: no].

--phylip

Assume infiles and outfiles are in PHYLIP format (instead of ALI format) [default: no].

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.