NAME
catfasta2phyml_raxmlPartitions.pl -- Concatenate FASTA alignments PHYLIP, generates partition for
RaXML and estimates best model test fitting each partition.
SYNOPSIS
catfasta2phyml_raxmlPartitions.pl [options] [files]
OPTIONS
-h, -?, --help
Print a brief help message and exits.
-m, --man
Prints the manual page and exits.
-c, --concatenate
Concatenate files even when number of taxa differ among
alignments. Missing data will be filled with all gap (-)
sequences.
-f, --fasta
Print output in FASTA format. Default is PHYML format.
-p, --phylip
Print output in a strict PHYLIP format. See
http://evolution.genetics.washington.edu/phylip/doc/sequence.htm
l.
Note: the current output format is not entirely strict. Left
to do is to efficiently print sequences in blocks of 10 characters.
Check output if using this option.
-s, --sequential
Print output in sequential format. Default is interleaved.
-output_file
File to print alignment concatenated.
-v, --verbose
Be verbose by showing some useful output. See the combination
with -n.
-n, --noprint
Do not print the concatenation, just check if all files have the
same sequence lables and lengths. Program returns 1 on exit. See
also the combination with -v.
-protest_jar
Java jar file for ProtTest3 (https://github.com/ddarriba/prottest3)
in order to generate best model fitting alingment for each partition.
-noProtTest
Do not estimate model for each partition. Adds -model_partition [string]
to every partition generated.
-model_partition
String provided will be
DESCRIPTION
This is a modification of the original script written by Johan A. A. Nylander,
catfasta2phym.pl.
This version is intended to generate a phylip file with as many partitions as
alignments provided each one containing the best protein model that fits according
to ProtTest3.
Please refer to https://github.com/nylander/catfasta2phyml for further details
of the original file.
The original catfasta2phyml.pl will concatenate FASTA alignments to one file
(interleaved PHYML or FASTA format) after checking that all sequences
are aligned (of same length). If there are sequence labels that are not
present in all files, a warning will be issued. Sequenced can, however,
still be concatenated (and missing sequences be filled with missing data
(gaps)) if the argument --concatenate is used.
Prints to STDOUT.
USAGE
This is a modification of the original script written by Johan A. A. Nylander,
catfasta2phym.pl. This version is intended to generate a phylip file with as many
partitions as alignments provided each one containing the best protein model that
fits according to ProtTest3.
Please refer to https://github.com/nylander/catfasta2phyml for the original file
and original options.
To concatenate fasta files to a phyml readable format, generate a partition for
each fasta file provided and estimate the best fitting model test.
catfasta2phyml.pl -p file*.fas -prottest_jar /path/to/prottest_bin/prottest_java_file.jar >> out.phy
To concatenate fasta files to a phyml readable format but do not generate a partition
for each fasta.
catfasta2phyml.pl -p file*.fas -noProtTest -model_partition LG
AUTHOR
Written by Johan A. A. Nylander
Modified by Jose F. Sanchez Herrero (2018)
DEPENDENCIES
Uses Perl modules Getopt::Long and Pod::Usage
LICENSE AND COPYRIGHT
Copyright (c) 2010, 2011, 2012, 2013, 2014, 2015, 2016 Johan Nylander. All
rights reserved.
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 2 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. http://www.gnu.org/copyleft/gpl.html
DOWNLOAD
https://github.com/nylander/catfasta2phyml
https://github.com/JFsanchezherrero/catfasta2phyml