Incomplete lineage
        sorting example

September 23, 2016: I have released a newer version of STELLS: v2.1.0, which contains the implementation of STELLS2. My tests show that STELLS2 is much faster than the original STELLS, while has about the same inference accuracy as STELLS. In the new release, by default, STELLS2 will be run instead of the original STELLS. Staring from this release, STELLS is moving to GitHub. Please go to the GitHub webpage for the new release and also all future updates. I will no longer update this page.

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. (This is the original paper developing the overall STELLS algorithm for the inference of species tree from gene tree topologies.)

Yufeng Wu, "A coalescent-based method for population tree inference with haplotypes", Bioinformatics, v31, p. 691-698, 2015. (This paper develops an extension of STELLS, called
STELLSH, for the inference of population tree, 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.).

Yufeng Wu, "An Algorithm for Computing the Gene Tree Probability under the Multispecies
Coalescent and its Application in the Inference of Population Tree", submitted for publication, 2015. (This is a recent paper for a faster algorithm when there are multiple gene lineages for small number of populations. It also includes a new approach for the population tree inference from pairwise population distances.)

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. It has also been extended for the inference of population trees from haplotypes. See my papers 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. 2.0.0 (released at: October 27, 2015).
Source code available (see below).
In case you want to build from source code, here is the code. Simply de-compress and type "make".

In case you are looking for older versions of STELLS, here is the version 1.6.1.