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catfasta2phyml

NAME

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

  • -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.

DESCRIPTION

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

USAGE

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

TIPS

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)!

AUTHOR

Written by Johan A. A. Nylander

DEPENDENCIES

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

LICENSE AND COPYRIGHT

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.

DOWNLOAD

https://github.com/nylander/catfasta2phyml