Downloading XHMM

The XHMM program and source code is currently available to download for academic use only.

Git repository

The XHMM Git repository contains the core C++ code in addition to various useful scripts. Specifically, the always up-to-date "development" zip file is found here.

The scripts include tools for:

• Visualization of the PCA and the called CNVs
• Conversion of XHMM's .xcnv format to PLINK's .cnv format

Installing XHMM

XHMM was developed assuming compilation on Linux with gcc version 4.4. Other requirements are the pthread and lapack C libraries.

[Also, to modify the command-line options, it is necessary to install Gengetopt (recommended version 2.22 or higher).]

Uncompress the xhmm zip file, where you want to install it:
unzip master.zip

Change to the xhmm directory:
cd statgen-xhmm-*

Run make to install the software (which starts by automatically compiling the included hmm++ library):
make

XHMM is developed by Menachem Fromer and Shaun Purcell at Mount Sinai School of Medicine, The Broad Institute of MIT and Harvard, Analytic and Translational Genetics Unit (ATGU) at Massachusetts General Hospital

Please send questions to: The XHMM users group.