NAME

tree-clan-splitter.pl - Extract clans (FASTA files) from trees based on taxonomic filters

VERSION

version 0.210200

USAGE

    tree-clan-splitter.pl --indir <dir> --taxdir <dir> --tree-suffix=<str>
        [optional arguments]

REQUIRED ARGUMENTS

--indir=<dir>

Path to input directory containing tree files.

--taxdir=<dir>

Path to local mirror of the NCBI Taxonomy database.

--tree-suffix=<str>

Suffix for finding trees in the defined working directory.

OPTIONAL ARGUMENTS

--otu[-file]=<file>

Path to artificial groups' file (user defined).

--taxa-list=<file>

Path to taxa list file for tax_labeler.

--og-regex=<str>

Regular expression for capturing ortholgous group name

--boot-threshold=<n>

Bootstrap threshold for filtering clans

--map-ids

Restore ids from a .idm file

--verbosity=<level>

Verbosity level for logging to STDERR [default: level.default]. Available levels range from 0 to 3.

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTOR

Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>

COPYRIGHT AND LICENSE

This software is copyright (c) 2021 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.