NAME
HmmCleaner.pl - Removing low similarity segments from your MSA
VERSION
version 0.180450
USAGE
HmmCleaner.pl <infiles> [-costs <c1> <c2> <c3> <c4> --changeID --noX --ali --log-only]
REQUIRED ARGUMENTS
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.
- -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.