HapCluster++ is a linkage disequilibrium mapping software based on coalescent theory. It is designed to identify genomic variations that are associated with complex traits using a robust and efficient approach.
HapCluster++ is a software package that leverages coalescent theory for linkage disequilibrium mapping. The program employs a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale gene mapping using high-density marker maps. HapCluster++ represents a C++ implementation of the method discussed in the paper below (the original implementation was in R).
The software is available as source code under the GNU General Public License (GPL) and binary versions as Linux RPM files. The source code has compiled successfully on various Linux and UNIX systems. As the developer has limited access to architectures other than Linux, binary distributions for other platforms will not be available unless someone is willing to build the distributions.
To build the source files, unzip and untar the file, then run 'configure' and finally 'make'. To install the program, run 'make install'. A 'make check' command can be run to test that the build was successful.
HapCluster++ is initiated via the command line, by inputting a file containing marker positions and a file containing phased haplotypes. The program then outputs samples from the posterior density of disease loci that can be analyzed in other software packages, such as R. The output's default behavior involves disease locus samples written to standard out, which can be redirected to a file using the option -o when using the program in verbose mode (option -v).
The program has undergone significant updates in HapCluster++ version 2.0 format, including a port to SNPFile version 2.0 format.
The software is available as source code under the GNU General Public License (GPL) and binary versions as Linux RPM files. The source code has compiled successfully on various Linux and UNIX systems. As the developer has limited access to architectures other than Linux, binary distributions for other platforms will not be available unless someone is willing to build the distributions.
To build the source files, unzip and untar the file, then run 'configure' and finally 'make'. To install the program, run 'make install'. A 'make check' command can be run to test that the build was successful.
HapCluster++ is initiated via the command line, by inputting a file containing marker positions and a file containing phased haplotypes. The program then outputs samples from the posterior density of disease loci that can be analyzed in other software packages, such as R. The output's default behavior involves disease locus samples written to standard out, which can be redirected to a file using the option -o when using the program in verbose mode (option -v).
The program has undergone significant updates in HapCluster++ version 2.0 format, including a port to SNPFile version 2.0 format.
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