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