University of Sydney, School of Biological Sciences

 

 

 

 

BH+I – A General Markov Model for Phylogenetic Analysis and Estimation of Invariant Sites

 

 

Description

BH+I is a java based program for maximum-likelihood analysis of nucleotide sequence evolution when the sequences contain invariant sites. It implements a model of the same name and makes the following assumptions:

  1. The aligned sites can be divided into two groups – variable and invariant
  2. The variable sites are independent and identically distributed and the process acting on each site is Markovian
  3. The proportion of A, C, G, and T among invariant sites is independent of the proportion of A, C, G, and T in variable sites

 

The BH+I model does not require the Markov processes acting on variables sites to be stationary, reversible or homogeneous.

 

Authors

Vivek Jayaswal – vivek@maths.usyd.edu.au

Lars Jermiin – lars.jermiin@usyd.edu.au

John Robinson – johnr@maths.usyd.edu.au

 

Citation

There is no published citation for this program as yet. Please e-mail the authors for information about citing this program.

 

License

Copyright (C) 2006 

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software foundation; either version 2 of the License, or (at your option) any later version.

 

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

 

Installation

This program requires JDK 1.4 or JDK 1.5 to be installed on the user’s system. Once Java is installed, the source code can be compiled on the system as follows:

 

  • Download and unzip the source code
  • Let C:/BHI/Java refer to the path of the Java files after unzipping. Set the classpath as follows:
    • Windows users  should type set classpath=%classpath%;C:/BHI/Java;
    • Unix users should type export CLASSPATH=$CLASSPATH:/BHI/Java
  • Make C:/BHI/Java the current directory
  • Compile the programs by typing javac BHI.java
  • Execute the programs by typing java BHI

 

Downloads

MANUAL

BH+I Source Code (Zip format)

Tree Viewer Source Code (Zip format)