First commit

README.md

@@ -1,4 +1,78 @@
 catfasta2phyml
 ==============
 
-Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file
+Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file
+
+
+NAME
+    catfasta2phyml.pl -- Concatenate FASTA alignments to PHYML or FASTA
+    format
+
+SYNOPSIS
+    catfasta2phyml.pl [options] [files]
+
+OPTIONS
+    -h, -?, --help
+            Print a brief help message and exits.
+
+    -m, --man
+            Prints the manual page and exits.
+
+    -f, --fasta
+            Print output in FASTA format. Default is PHYML format.
+
+    -r, --relaxed-phylip
+            Print output in relaxed PHYLIP format. That is, sequence labels
+            are only printed once, and, the "relaxed", labels can have more
+            than 8 characters.
+
+    -v, --verbose
+            Be verbose.
+
+    -d, --dont-print
+            Do not print the concatenation. Program returns 1 on exit.
+
+DESCRIPTION
+    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.
+
+USAGE
+    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
+
+AUTHOR
+    Written by Johan A. A. Nylander
+
+DEPENDENCIES
+    Uses Perl modules Getopt::Long and Pod::Usage
+
+LICENSE AND COPYRIGHT
+    Copyright (c) 2010, 2011, 2012 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
+