Introduction

This is a home page for PhaseMachine. It is a program for analysis of biological populations through Support Vector Machine (SVM) classification of nucleotide sequence data. PhaseMachine classifies sequences generated by PHASE haplotype inference program.

PhaseMachine is written in C++ programming language. The distribution contains pre-compiled binaries for Linux and Windows.

Licensing

PhaseMachine is licensed under MIT license (also known as X11 license), which allows unrestricted use for any purpose.

Downloading and Installing

Click here to download PhaseMachine (choose the most recent release and click on `Download ...' link). Linux users, download file with extension .tar.gz and untar/gunzip the downloaded file. Windows users, please download file with .zip extension. After unpacking, the executable PhaseMachine can be found in bin subdirectory. Source code is in the src subdirectory. Documentation is in the doc subdirectory. data subdirectory contains sample data files ed.dat and ad.dat. Sample batch script is in samples/platform subdirectory, where `platform' is either `linux' or `windows'.

Authors

PhaseMachine was written by Martin Eggenberger and Zhihong He of the Center for Computing in Life Sciences at San Francisco State University, under direction of Ljubomir Buturovic, Sarah Cohen and Dragutin Petkovic. Please send all comments and bug reports to meggenbe@sfsu.edu

Acknowledgements

The authors acknowledge and wish to thank Chih-Chung Chang and Chih-Jen Lin, authors of Support Vector Machine library LIBSVM, and people at VA Software for their support of open source software.