vPhyloMM

Description

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.

Installation

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.

Steps:

  1. Extract vPhyloMM
  2. Install Sliding MinPD (see documentation/Installation/Sliding_MinPD.pdf)
  3. Install R (see R.pdf)
  4. Install msm for R (see R_Libraries.pdf)
  5. Install GraphViz (see GraphViz.pdf)
  6. Install ActivePerl v 5.10.0 build 1005 or newer (see ActivePerl.pdf)
  7. Install Perl Modules (see Perl_Modules.pdf)
  8. Move on to "Getting Started" shown below.

To learn more about how to use vPhyloMM read the documentation at:

perldoc Run_vPhyloMM.pl

Reference

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.

Last updated: 7/31/2009