/ 
Bio-MUST-Apps-HmmCleaner-0.180750
River stage zero No dependents
/ HmmCleaner.pl

NAME

HmmCleaner.pl - Removing low similarity segments from your MSA

VERSION

version 0.180750

USAGE

HmmCleaner.pl <infiles> [-costs <c1> <c2> <c3> <c4> --changeID --noX --ali --log-only]

REQUIRED ARGUMENTS

<infiles>

list of alignment file to check with HmmCleaner

OPTIONS

-costs <c1> <c2> <c3> <c4>

Cost parameters that defines the low similarity segments detected by HmmCleaner. Default values are -0.15, -0.08, 0.15, 0.45 Users can change each value but they have to be in increasing order. c1 < c2 < 0 < c3 < c4 Predefine value are also available with --large and --specificity options but user defined costs will be prioritary if present.

--changeID

Determine if output will have defline with generic suffix (_hmmcleaned)

--noX

Convert X characters to gaps that will not be taken into account by HmmCleaner.

-symfrac <symfrac>

Handle the symfrac option of hmmbuild modifying the required fraction of sequences to consider a position as a consensus column

-profile=<profile>

Determine how the profile will be create complete or leave-one-out (default: complete) leave-one-out = without the analyzed sequence (new profile each time) complete = all sequences (same profile for each sequence) First case is more sensitive but need more ressources (hence more time)

--large

Load predifined cost parameters optimized for MSA with at least 50 sequences. Can be use with --specificity option. User defined costs will be prioritary if present.

--specificity

Load predifined cost parameters optimized to give more weigth on specificity. Can be use with --large option. User defined costs will be prioritary if present.

--log_only

Only outputs list of segments removed.

--ali

Outputs result file(s) in ali MUST format.

-v[erbosity]=<level>

Verbosity level for logging to STDERR [default: 0]. Available levels range from 0 to 5.

--version
--usage
--help
--man

Print the usual program information

AUTHOR

Arnaud Di Franco <arnaud.difranco@gmail.fr>

COPYRIGHT AND LICENSE

This software is copyright (c) 2018 by Arnaud Di Franco.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.