Version 4.1.5
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Programs

When installing the package seq++, both the libary and a set of binary programs are available on your system:
  1. estim_m is dedicated to Phased Markov model estimation (based on the PhasedMarkov object).
  2. estim_vlm is dedicated to Variable Length Markov model estimation (based on the PhasedVLMarkov object).
  3. estim_pm is dedicated to Parcimonious Markov model estimation (based on the PhasedPMarkov object).
  4. estim_mtd is dedicated to Mixture Transition Distribution Markov model estimation (based on the PhasedMTDMarkov object).
  5. simul_m is dedicated to sequence simulation from a markovian matrix (previously estimated) or a base sequence (based on the PhasedMarkov object).
  6. dist_m computes the Total Variation Distance between two Markov models previously estimated with estim_*.

Nota bene: the estim_* programs differs only on the way the estimation of the markovian matrix is performed.

Basicaly the best way to discover the possibilities of these programs is the Unix way:

program_name --help  OR man program_name

The estimation results can be saved in such a representation:

# 1 <- Order of the phased Markov chain
# 2 <- Phase
# 4 <- Alphabet size
# Phase n°0
# Transition matrix:
0.3945322543    0.1652811616    0.1535033485    0.2866832356
0.2758032675    0.208204727     0.2605722039    0.2554198016
0.3496152294    0.2310568942    0.1708121974    0.248515679
0.2312234494    0.2503993203    0.1515293118    0.3668479184
# Stationnary Probability:
0.3127105148    0.2114684268    0.1783495332    0.2974715251
# Phase n°1
# Transition matrix:
0.3923961961    0.163516403     0.1521005152    0.2919868858
0.2789719005    0.2082462898    0.2570550517    0.2557267579
0.352109549     0.2297549901    0.1679259742    0.2502094867
0.2320996136    0.2447917561    0.1520437956    0.3710648347
# Stationnary Probability:
0.3135417652    0.2089660861    0.1771006767    0.300391472



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Generated on Thu Aug 4 18:34:05 2005 for seqpp by doxygen 1.3.9.1