cm2hmm1

Usage

Overview

cm2hmm reads a covariance model (CM) from cmfile, constructs a hidden-Markov model (HMM) that preserves some information of the CM and saves the HMM to hmmfile. The HMM can be used as a rigorous pre-filtering step to searching with the CM.

The CM file must be in the standard format output used by Infernal.

Options

--help

Print brief help; includes summary of command-line parameters.

background [background parameters]

Select the model of background sequence. uniform gives all bases equal probability (25%). gc <fraction> specifies the G+C content. <fraction> should be a number between 0 and 1. file <filename> loads the base distribution from a file in a specific format.

HMMtype

Specify the type of HMM to be used; options are compact and expanded. Compact-type models are generally faster, but expanded-type models may provide better filtering.

optimizer [optimizer parameters]

Specify which mathematical optimizer is to be used to create the final model. Currently the only option is cfsqp which takes two paramters: <B> <C>. B=0, C=1 are reasonable choices. (See the CFSQP manual for further details.)