simul_m

Langue: en

Version: 113521 (mandriva - 01/05/08)

Section: 1 (Commandes utilisateur)

Sommaire

NAME

simul_m - Markov model simulation tool

SYNOPSIS

simul_m arguments [options]

DESCRIPTION

simul_m is a program that generates a sequence of tokens using the Markov model given as input. This Markov model can be calculated using the estim_m program or the estim_pm program.

ARGUMENTS

-m --model=FILENAME
Input file containing the Markov model parameters.
-l --length=INTEGER
Length of the sequence to be generated.

OPTIONS

-a --alphabet=FILENAME
A file describing the alphabet to use (DNA alphabet, default setting).
-A --Alphabet=EXPRESSION
An expression describing the alphabet to use: [number<10 of characters for each pattern]+[:]+[alphabet patterns list] (DNA alphabet, default setting).
--dna
Use DNA alphabet (1:AGCT, default setting).
--protein
Use amino acid alphabet (1:IVLFCMAGTWSYPHEQDNKR).
-o --output=FILENAME
Simulated sequence file. (seq.simul, default setting).
-v --version
Display the version number and exit.
-h --help
Print this help and exit.

Examples

Generate a sequence of 100000 tokens using the model contained in the model.desc file. Store the result in file sequence.dat.

simul_m -l 100000 -m model.desc -o sequence.dat

Generate a sequence of 100000 tokens using the model contained in the mod2.desc file. The alphabet of the sequence tokens is contained in the custom.alpha file. Store the result in file seq2.dat.

simul_m -l 100000 -m mod2.desc -a custom.alpha -o seq2.dat

AUTHORS

simul_m is part of the seq++ package, developed by Vincent Miele <miele@genopole.cnrs.fr>, David Robelin <robelin@genopole.cnrs.fr>, Pierre-Yves Bourguignon <bourguignon@genopole.cnrs.fr>, Gregory Nuel <nuel@genopole.cnrs.fr> and Hugues Richard <richard@genopole.cnrs.fr>.

SEE ALSO

estim_m(1), estim_mtd(1), estim_pm(1), estim_vlm(1), dist_m(1)

More information on seq++ is available at <http://stat.genopole.cnrs.fr/seqpp>.