NAME

change-ids-ali.pl - Abbreviate or restore the org component of full seq ids in ALI files

VERSION

version 0.240390

USAGE

change-ids-ali.pl <infiles> --org-mapper=<file> --mode=<dir>
    [optional arguments]

REQUIRED ARGUMENTS

<infiles>

Path to input ALI files [repeatable argument].

--org-mapper=<file>

Path to the IDM file listing the long_org => abbr_org pairs.

--mode=<dir>

Direction of the id changing operation. The following directions are available: long2abbr and abbr2long.

OPTIONAL ARGUMENTS

--out[-suffix]=<suffix>

Suffix to append to infile basenames for deriving outfile names [default: none]. When not specified, outfile names are taken from infiles but original infiles are preserved by being appended a .bak suffix.

--[no]guessing

[Don't] guess whether sequences are aligned or not [default: yes].

--store-id-mapper

Store the IDM file corresponding to each output file [default: no].

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.