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
1. "Argument list too long" error?
If we run into the issue of "Argument list too long" (where we have a command
line longer than allowed on our system (getconf ARG_MAX) - which may happen
if we try to concatenate many files), we can still do it, but in steps. For
example (here with some help of GNU
parallel):
$ catfasta2phyml.pl -c $(find . -type f -name '*.ali') > concatenated.phy 2>/dev/null
-bash: catfasta2phyml.pl: Argument list too long
Instead, start by concatenating to intermediate files using GNU parallel
$ find . -type f -name '*.ali' | \
parallel -N1000 'catfasta2phyml.pl -c -f '"{}"' > tmp.'"{#}"'.conc'
Then concatenate the intermediate files to one
$ catfasta2phyml.pl -c tmp.*.conc > concatenated.phy 2>/dev/null
$ rm tmp.*.conc
2. But I want to split, not concatenate!
Facing the "opposite" situation (having a large concatenated fasta file that you want to split into individual alignments)? If you have a corresponding partitions file, you may give EAR a try (https://github.com/nylander/EAR)!
Written by Johan A. A. Nylander
Uses Perl modules Getopt::Long and Pod::Usage
Copyright (c) 2010-2020 Johan Nylander
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.