Software accompaniment to
Yufeng Wu,  "A Coalescent-based Method for Population Tree Inference with Haplotypes" , Bioinformatics, in press, 2014.

STELLSH is a program for finding the maximum likelihood estimate of the population tree (i.e. population split history) for the given population haplotypes. STELLSH assumes the infinite sites model of mutations, and no intra-locus recombination. STELLSH does not explicitly address gene flow and admixture. Simulation shows that the STELLSH is reasonably robust when there is some deviation from the model assumptions. See my paper for more details.

Current version: v. 1.0. (released at: October 22, 2014).
You need to first install the original STELLS program. Note: Files can be downloaded using "Save Link/Target As..."