catfasta2phyml.pl (.tgz file) -- Concatenate FASTA alignments to PHYML or FASTA format
catfasta2phyml.pl [options] [files]
Print a brief help message and exits.
Prints the manual page and exits.
Print output in FASTA format. Default is PHYML format.
Print output in relaxed PHYLIP format. That is, sequence labels are only printed once, and, the "relaxed", labels can have more than 8 characters.
Be verbose.
Do not print the concatenation. Program returns 1 on exit.
catfasta2phyml.pl will concatenate FASTA alignments to one file (interleaved PHYML or FASTA format) after checking that all sequence labels are present in all files, and that sequences are aligned (of same length).
Prints to STDOUT.
To concatenate fasta files to a phyml readable format:
catfasta2phyml.pl file1.fas file2.fas > out.phy
catfasta2phyml.pl *.fas > out.phy
catfasta2phyml.pl --verbose *.fas > out.phy
To concatenate fasta files to fasta format:
catfasta2phyml.pl -f file1 file2 > out.fasta
catfasta2phyml.pl -f *.fas > out.fasta
To check fasta alignments
catfasta2phyml.pl --dont-print --verbose *.fasta
catfasta2phyml.pl -d *.fasta
Written by Johan A. A. Nylander
Uses Perl modules Getopt::Long and Pod::Usage
Copyright (c) 2010, 2011 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