Software accompaniment to
Yufeng Wu, "Coalescent-based
Species Tree Inference from Gene Tree Topologies Under
Incomplete Lineage Sorting by Maximum Likelihood" [Link], Evolution, v. 66 (3), p. 763-775, 2012.
Oct. 22, 2014:
I have implemented an extension called STELLSH
to STELLS, which takes population haplotypes as input and
infer the population split history (called population tree).
This allows the inference from sequences directly, and may be
a better choice when the time scale is shorter. For more
details, see my paper to appear in Bioinformatics: "A Coalescent-based Method for Population
Tree Inference with Haplotypes".
STELLS is a program for finding the maximum likelihood
estimate of the species tree for the given gene trees, which
undergo incomplete lineage sorting (as illustrated in the above
figure). STELLS can also compute the gene tree probability for a
given species tree. See my paper for more details.
Note: Files can be downloaded using "Save
As..." After downloading the softwares, you may need to
change file access permissions (e.g. chmod u+x stells-linux).
Current version: v. 1.6.1 (released at: February 22, 2014). Source