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logiciels:drimm:help

# Help DRIMM

This program is dedicated to the estimation and the use of Drifting Markov Models (DMM).

## Two different ways to use

1. DMM is estimated on a sequence.
2. DMM is given in a model file.

## Description of parameters

-SpM Estimation by splines M. -N must be used.

-SpH Estimation by splines H. -N and -Nar must be used.

-Spl Estimation by splines. -N and -Nar must be used.

-Poly Estimation by polynom (stochastic matrices).

-PolyM Estimation by polynom (no stochastic matrices).

-out <basename> Basename for all output files. Output 'basename.config_<num>.out' with -s. Output 'basename.config_sm.out' with -sm. Output 'basename.config_ss.out' with -ss. Output 'basename.config.out' with -cf.

-a <alphabet_file> A file describing the alphabet to use.

-s <sequence_file>A file containing file of sequences. DMM is estimated on each sequence (Use 1). At least one of -s or -sm or -ss must be used

-sm <sequence_mean_file> A file containing file of sequences. DMM is estimated as a mean of DDM on each sequence (Use 1). At least one of -s or -sm or -ss must be used

-ss <sequence_sum_file> A file containing file of sequences. DMM is estimated over all the sequences (Use 1). At least one of -s or -sm or -ss must be used

-order <order>=0>Order of the DMM (Use 1). Order must be > 0 with -SpM or -SpH.

-deg <degree>=0> Degree of the DMM (Use 1). Degree is useless with -SpH and -Spl. Degree is 3.

-N <Number of segments>0> Number of segments in the case of estimation by splines.

-Nar <Number of segments>0> Number of aller retour with -Spl and -SpH.

-cf <model_file> DMM is given by the <model_file> (Use 2). Must be used with -Poly, -PolyM, -Spl, -SpM, or -SpH.

-L Compute the log-likelihood on the estimated sequences (Use 1). Can not be used with -sm or -ss

-AIC Compute the AIC on the estimated sequences (Use 1). Can not be used with -sm or -ss

-BIC Compute the BIC on the estimated sequences (Use 1). Can not be used with -sm or -ss

-l <sequence_file_l> Compute the log-likelihood on <sequence_file_l>.

-aic <sequence_file_aic>Compute the aic on <sequence_file_aic>.

-bic <sequence_file_bic> Compute the bic on <sequence_file_bic>.

-law Compute the stationary law of the DMM. basename.trace_stat_<num>.out is an output containing the stationary law. <num> is an integer designing the number of the sequence.

-slaw <in>0> <out>0> Compute the stationary law of the DMM between <in> and <out>. basename.trace_stat_segment_<num>.out is an output containing the stationary law. <num> is an integer designing the number of the sequence.

-dist Compute distributions of the DMM. basename.trace_dist_<num>.out is an output containing the distributions. <num> is an integer designing the number of the sequence.

sdist <in>0> <out>0> Compute the distribution of the DMM between <in> and <out>. basename.trace_dist_segment_<num>.out is an output containing the distributions. <num> is an integer designing the number of the sequence.

-pi Return files 'basename.Pit_<num>.out' or 'basename.Pit_sm.out' or basename.Pit.out' or 'basename.Pit_ss.out' containing the matrix Pi_t for all t. <num> is an integer designing the number of the sequence

-simu Return files 'basename.simulation_<num>.out' or 'basename.simulation_sm.out' or 'basename.simulation_ss.out' or basename.simulation.out' containing a sequence simulated by the DMM. <num> is an integer designing the number of the sequence.

-nv Mode 'not verbose'.

-h Print this help.

## Examples

DRIMM -Poly -order 1 -deg 2 -a dna.alpha -s lambda.fa -out lambda

for the estimation of a polynomial DMM (order 1 and degree 2) on the phage Lambda.

DRIMM -SpM -N 2 -order 1 -deg 3 -a dna.alpha -s lambda.fa -out lambda

for the estimation of a DMM with polynomial splines (order 1 and degree 3 with 2 segments) on the phage Lambda.