Software accompaniment to
Yufeng Wu, "A Coalescent-based Method for Population Tree
Inference with Haplotypes"
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
the main part of STELLSH is
implemented in the STELLS program. You will also need these
scripts and tools to use STELLSH
effectively. It also includes some examples.