MtreeHMM

Mutagenetic tree hidden Markov models

Current version

0.1.01 Jul 2006

Description

MtreeHMM is a Perl program that implements the Expectation Maximization algorithm described in (Beerenwinkel & Drton, 2007) for estimating the parameters of the mutagenetic tree hidden Markov model from longitudinal clonal sequence data.

Download

MtreeHMM is distributed under the GNU General Public License.

• mtreehmm-0.1.01 Jul 2006
  (includes source code, toy example, and HIV data set)

Installation and Usage

In order to run MtreeHMM you need, besides the Perl interpreter, the Perl module 'Amoeba.pm' available at CPAN. At the beginning of the PERL script, change the line

use lib "$ENV{HOME}/perllib";

to point to the directory that contains 'Math/Amoeba.pm' (here '~/perllib').

The input data needs to be specified in four different files that share the same filestem:

filestem.model - Mutagenetic tree model, adjacency matrix
filestem.pat - List of binary mutational patterns (clones)
filestem.patient - List of patients
filestem.week - List of time points

The '.model' and '.pat' files are the same as in the Mtreemix package. You may use Mtreemix to estimate the tree structure ('.model' file) from the observed mutational patterns ('.pat' file).

After download and unpacking, type 'mtreehmm.pl -h' for detailed usage instructions. The download package includes a small test dataset named toy, from which the file formats become apparent.

The HIV data set analyzed in (Beerenwinkel & Drton, 2007) is also included.

Authors and Contributors

• Niko Beerenwinkel
• Mathias Drton

Citation

• Beerenwinkel N, Drton M (2007). A mutagenetic tree hidden Markov model for longitudinal clonal HIV sequence data. Biostatistics 8(1):53-71.

Contact

Niko Beerenwinkel