Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial HMMs

Dirk Husmeier
Biomathematics and Statistics Scotland (BioSS)
JCMB, The King's Building, Edinburgh EH9 3JZ, United Kingdom

Warning

Please check the errata webpage for bugs and updates.

Software

You can download a free software package written in MATLAB for simulating phylogenetic factorial HMMs, as described in Bioinformatics 21: ii166-ii172. The programs invoke functions of the HMM Toolbox written by Kevin Murphy; so you need to download his software package first. To download the version of the HMM toolbox that was used for the present software implementation, click here. Note that my software was developed solely as a model exploration tool, and it is provided without guarantee of maintenance or support, and without warranty. The copyright holder is not liable for any damages which may result in any manner from the use of this software. You can download the software package as a gzipped TAR file. To extract this file under UNIX, proceed as follows:

gunzip Barge.tar.gz tar xvf Barge.tar

You can now delete the TAR file:

rm Barge.tar

Make sure you add the directory with the programs to your MATLAB path. You can do this from the MATLAB prompt as follows:

Barge_HOME='XXX'; eval(sprintf('addpath ''%s'' ', Barge_HOME));

where XXX is the name of the directory in which you keep the Barge programs. The software package contains several functions, called Barge_XXXX.m (where XXXX are different names). Information about each function is obtained by typing help plus the function name (without the extension ".m") at the MATLAB prompt.

help Barge_XXXX

Example

Here is an example program.

Data

Matlab program for generating the synthetic data, which calls the MATLAB functions Mutation.m, Kimura2PM.m, and SampleFromMultinomial.m.
Neisseria sequence alignment
Maize actin gene sequence alignment

Note that the sequences are in SERAD format.

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