NAME

forty-two.pl - The Answer to the Ultimate Question of Phylogenomics

VERSION

version 0.190820

USAGE

forty-two.pl <infiles> --config=<file> [optional arguments]

REQUIRED ARGUMENTS

<infiles>

Path to input ALI files [repeatable argument].

forty-two should not be called in a shell loop. If so it will run very slowly, especially when using tax filters (because loading the NCBI Taxonomy database is quite long). Use shell jokers instead:

forty-two.pl --config=config.yaml rpl*.ali rps*.ali

--config=<file>

Path to the configuration file specifying the run details.

In principle, several configuration file formats are available: XML, JSON, YAML. However, forty-two was designed with YAML in mind. See the test directory of the distribution for annotated examples of YAML files.

OPTIONAL ARGUMENTS

--verbosity=<level>

Verbosity level for logging to STDERR [default: 0]. Available levels range from 0 to 6. Level 6 corresponds to debugging mode.

--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.