NAME

frameshiftSimul_final.pl - Simulation for HmmCleaner

VERSION

version 0.180750

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>

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.