HapReads

Software accompaniment to 

Haplotype Inference from Short Sequence Reads Using a Population Genealogical History Model, Jin Zhang and Yufeng Wu, in proceedings of Pacific Symposium on Biocomputing: 288-299, 2011. link

HapReads is a ILP program for infering haplotypes with shot reads, which finds the most likely haplotypes by approximating local genealogical history as a perfect phylogeny. See the paper for more details.

HapReadsGLPKMac, executable compiled under Mac Os X with GLPK.

HapReadsGLPK32, executable compiled under 32 bits Linux with GLPK.

HapReadsGLPK64, executable compiled under 64 bits Linux with GLPK.

HapReadsCPLEX64, executable compiled under 64 bits Linux with CPLEX.

Demo

HapReads.tar.gz, a compressed file contains all the above files