Incomplete lineage
        sorting example
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 Link/Target 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 code available (see below).
In case you want to build from source code, here is the code. Simply de-compress and type "make".