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.