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:


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



Installing / using the XHMM R scripts

The XHMM R code is now available as an R library. There are still two options for using the scripts:

Newer (preferred) option


Older option

Directly source the R code found in the downloaded source code, by running the following at the top of your R scripts:
XHMM_PATH = "./"
XHMM_SCRIPTS_PATH = paste(XHMM_PATH, "/sources/scripts/R_functions", sep="")
source(paste(XHMM_SCRIPTS_PATH, "/sourceDir.R", sep=""))
sourceDir(XHMM_SCRIPTS_PATH, trace = FALSE, recursive = TRUE)

library(gplots)
library(plotrix)