NAME

prune-outliers.pl - Identify and discard outliers based on all-versus-all BLAST searches

VERSION

version 0.213470

USAGE

        prune-outliers.pl <indirs> [options]

REQUIRED ARGUMENTS

<indirs>

Path to input directories containing ALI (or FASTA) files [repeatable argument].

OPTIONS

--evalue=<n>

evalue threshold for a hit to be considered during the all-versus-all BLAST searches [default: n.default].

--min-ident=<n> | --min_ident=<n>

Minimal identity value used for selecting sequences that match at least this proportion in the all-versus-all BLAST searches [default: n.default]. An output dir will be created by step of 0.1 between the min threshold and max threshold.

--max-ident=<n> | --max_ident=<n>

Maximum percent value used for selecting sequences that match at least this proportion in the all versus all BLAST searches [default: n.default]. An output dir will be created by step of 0.1 between the min threshold and max threshold.

--min-hits=<n> | --min_hits=<n>

Minimum number of hits in the all-versus-all BLAST searches required for a sequence to be retained in the output file [default: n.default].

--[no]guessing

[Don't] guess whether sequences are aligned or not [default: yes].

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTORS

• Amandine BERTRAND <amandine.bertrand@doct.uliege.be>

• Loic MEUNIER <loic.meunier@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.