RENT example
Software accompaniment to
Yufeng Wu, New Methods for Inference of Local Tree Topologies with Recombinant SNP Sequences in Populations, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(1):182-193, 2011.

RENT is a program for inferring local tree topologies from recombinant SNP haplotypes. The motivation is that, due to meiotic recombination, evolutionary history of population sequences is not a single tree. Instead, the population genealogical history may change along the genome. RENT is designed to find these changing genealogical trees (called local trees). See my paper for more details.

Note: Files can be downloaded using "Save Link/Target As..." After downloading the softwares, you may need to change file access permissions (e.g. chmod u+x stells-linux). Source code is available upon request .

Current version: beta v. 0.1. Source code available upon request.