NAME

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

VERSION

version 0.213470

USAGE

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

REQUIRED ARGUMENTS

<infiles>

Path to input ALI (or FASTA) 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

--threads=<n>

Number of threads to run in parallel [default: n.default]. Parallelization is achieved by processing several ALI files in parallel using an internal queue. Therefore, the specified number of threads should not be larger than the number of input ALI files.

--outdir=<dir>

Optional output dir that will contain the enriched ALI files and/or taxonomic reports (will be created if needed) [default: none]. Otherwise, output files will be written in the same directory as input files.

--verbosity=<level>

Verbosity level for logging to STDERR [default: level.default]. 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>

CONTRIBUTOR

Mick VAN VLIERBERGHE <mvanvlierberghe@doct.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.