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BH – A
General Markov Model for Phylogenetic Analysis
Description
BH is a java based program for maximum-likelihood analysis of nucleotide sequence evolution. It assumes that each aligned site is independent and identically distributed and the process acting on each site is Markovian. However, unlike the family of time-reversible models, it does not require the Markov process 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
Jayaswal, V., L. S. Jermiin, and J. Robinson. 2005. Estimation of phylogeny using a general Markov model. Evolutionary Bioinformatics Online 1: 62-80.
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:/BH/Java refer to the path of the Java files after unzipping. Set the classpath as follows:
- Windows users should type set classpath=%classpath%;C:/BH/Java;
- Unix users should type export CLASSPATH=$CLASSPATH:/BH/Java
- Make C:/BH/Java the current directory
- Compile the programs by typing javac BH.java
- Execute the programs by typing java BH
Downloads