HmmCleaner.pl - Removing low similarity segments from your MSA
version 0.180750
HmmCleaner.pl <infiles> [-costs <c1> <c2> <c3> <c4> --changeID --noX --ali --log-only]
list of alignment file to check with HmmCleaner
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.
Determine if output will have defline with generic suffix (_hmmcleaned)
Convert X characters to gaps that will not be taken into account by HmmCleaner.
Handle the symfrac option of hmmbuild modifying the required fraction of sequences to consider a position as a consensus column
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)
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.
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.
Only outputs list of segments removed.
Outputs result file(s) in ali MUST format.
Verbosity level for logging to STDERR [default: 0]. Available levels range from 0 to 5.
Print the usual program information
Arnaud Di Franco <arnaud.difranco@gmail.fr>
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.
To install Bio::MUST::Apps::HmmCleaner, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::MUST::Apps::HmmCleaner
CPAN shell
perl -MCPAN -e shell install Bio::MUST::Apps::HmmCleaner
For more information on module installation, please visit the detailed CPAN module installation guide.