NAME
frameshiftSimul_final.pl - Simulation for HmmCleaner
VERSION
version 0.243280
USAGE
frameshiftSimul_final.pl <infiles> --taxdir=<taxdir> [--noX --noStop -nf <nf> -sf <sf> -rep <rep> --profile=<profile>]
REQUIRED ARGUMENTS
- <infiles>
-
list of alignment file to check with HMMCleaner
- --taxdir=<taxdir>
-
Path to local mirror of the NCBI Taxonomy database as obtain from setup-taxdir.pl
OPTIONS
- -t[hreshold] <threshold>
-
threshold value determining shifts in sequence compare to HMM model
- -cost1=<cost1>
-
cost of blank character in profile alignment
- -cost2=<cost2>
-
cost of + character in profile alignment
- -cost3=<cost3>
-
cost of lowercase character in profile alignment
- -cost4=<cost4>
-
cost of uppercase character in profile alignment
- -nf <nf>
-
number of frameshift
- -sf <sf>
-
size of frameshift
- -rep <rep>
-
number of replicate for one file
- -subset <subset>
-
number of seq to keep in file at random
- --noX
-
Determine that X characters don't have to be consider by HMMER
- --noStop
-
Not stopping translation at STOP codon
- -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>
CONTRIBUTOR
Denis BAURAIN <denis.baurain@uliege.be>
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.