catfasta2phyml.pl -- Concatenate FASTA alignments to PHYML, PHYLIP, or FASTA format

catfasta2phyml.pl [options] [files]

• -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.

• -i, --intersect

  Concatenate sequences for sequence labels occuring in all input files (intersection).

• -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.html.

  Note: The current output is not entirely strict for the interleaved format. Left to do is to efficiently print sequences in blocks of 10 characters. The sequential PHYLIP format works, on the other hand (use -s in combination with -p).

• -s, --sequential

  Print output in sequential format (default is interleaved).

• -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.

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.

In addition, only sequences with sequence labels present in all files (the intersection) can be printed using the --intersect argument.

The program prints the concatenated data to STDOUT. A table with information about partitions is printed to STDERR. Example:

file1.fas = 1-625
file2.fas = 626-1019
file3.fas = 1020-2061
file4.fas = 2062-3364
file5.fas = 3365-3796

To concatenate fasta files to a phyml readable format:

catfasta2phyml.pl file1.fas file2.fas > out.phy
catfasta2phyml.pl *.fas > out.phy 2> partitions.txt
catfasta2phyml.pl --sequential *.fas > out.phy
catfasta2phyml.pl --verbose *.fas > out.phy

To concatenate fasta files to fasta format:

catfasta2phyml.pl -f file1.fas file2.fas > out.fasta
catfasta2phyml.pl -f *.fas > out.fasta

To check fasta alignments:

catfasta2phyml.pl --noprint --verbose *.fas
catfasta2phyml.pl -nv *.fas
catfasta2phyml.pl -n *.fas

To concatenate fasta files, while filling in missing taxa:

catfasta2phyml.pl --concatenate --verbose *.fas

To concatenate sequences for sequence labels occuring in all files:

catfasta2phyml.pl --intersect *.fas

Written by Johan A. A. Nylander

Uses Perl modules Getopt::Long and Pod::Usage

Copyright (c) 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018 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

https://github.com/nylander/catfasta2phyml