The purpose of this software is to generate a transition model showing the
mutational pathways of drug resistance for viruses under drug pressure. The
input to the program is a set of aligned DNA fasta files, one per patient, for
patients under a specific therapy X. Each fasta file should be labeled
by the patient number and must contain serially-sampled viral clonal
sequences. A "markers" file containing the positions and amino acids
associated with drug resistance for therapy X is also needed.
A Detailed
description of how to prepare sequences for running in vPhyloMM is
available under Links below.The output
of the program is a matrix showing the transition probabilities between
different viral genotypes for a particular time interval and\or a graph
(if GraphViz was installed) showing the transition model. Other output options
that generate statistics of the model are also available.
Installation, user manual and sample files are included in the tar.gz file.
Detailed installation steps for Windows and UNIX/LINUX are included
under the 'Documentation/Installation' directory. Note that
to use the GUI, the user will need to install ActiveState's ActivePerl
(http://www.activestate.com/activeperl) distribution as the standard
distribution is not compatible with Tcl/Tk.
The creation of graphs requires the additional installation of GraphViz and the GraphViz perl module. These are optional if vPhyloMM is not going to be used to graph transition states.
To learn more about how to use vPhyloMM read the documentation at:
perldoc Run_vPhyloMM.pl
Getting Started: To get started
using vPhyloMM.
Preparing Sequences: To read
about how to prepare sequences for use with vPhyloMM.
Buendia, P., Cadwallader, B. and DeGruttola, V. (2009)
A phylogenetic and Markov model approach for the reconstruction of
mutational pathways of drug resistance. Bioinformatics,
In Press.