NAME

split-rates-ali.pl - Split ALI files into subsets of sites based on evolutionary rates

VERSION

version 0.203490

USAGE

split-rates-ali.pl <infiles> [optional arguments]

REQUIRED ARGUMENTS

<infiles>

Path to input RATES files [repeatable argument].

OPTIONAL ARGUMENTS

--in[-strip]=<str>

Substring(s) to strip from infile basenames before attempting to derive other infile (e.g., ALI files) and outfile names [default: none].

--out[-suffix]=<suffix>

Suffix to append to (possibly stripped) infile basenames for deriving outfile names [default: none]. When not specified, outfile names are taken from infiles but original infiles are preserved by being appended a .bak suffix.

--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].

--other-rates=<file>

Optional additional rates file of the same length as the main infile(s) that will be used to compute rate deltas [default: none]. Currently, rate deltas are defined as the absolute difference between the two rates at each site. This could be improved by, e.g., computing relative deltas.

--bin-number=<n>

Number of bins to define [default: 10].

--percentile

Define bins containing an equal number of sites rather than bins of equal width in terms of rates [default: no].

--cumulative

Define bins including all previous bins [default: no]. This leads to ALI outfiles of increasing width and only makes sense when slower sites are in lower bins. If higher "rates" mean slower sites, use the --descending option.

--descending

Reverse bin order to accommodate "rates" files where higher values actually correspond to slower sites, such as those produced by Carla Cummins' TIGER [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.