NAME

tax-filter-ali.pl - Apply a taxonomic filter to ALI files

VERSION

version 0.211470

USAGE

    tax-filter-ali.pl --filter=<file> --taxdir=<dir> <infiles>
        [optional arguments]

REQUIRED ARGUMENTS

<infiles>

Path to input ALI files [repeatable argument].

--filter=<file>

Path to an IDL file specifying the taxonomic filter to be applied.

In a tax_filter, wanted taxa are to be prefixed by a '+' symbol, whereas unwanted taxa are to be prefixed by a '-' symbol. Wanted and unwanted taxa are linked by logical ORs.

An example IDL file follows:

    -Viridiplantae
    -Opisthokonta
    +Ascomycota
    +Oomycota
--taxdir=<dir>

Path to local mirror of the NCBI Taxonomy database.

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.

--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.