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Bioinformatics. 2009 Apr 1;25(7):971-3. doi: 10.1093/bioinformatics/btp079. Epub 2009 Feb 10.

STEM: species tree estimation using maximum likelihood for gene trees under coalescence.

Author information

  • 1Departments of Statistics and Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA. lkubatko@stat.osu.edu

Abstract

STEM is a software package written in the C language to obtain maximum likelihood (ML) estimates for phylogenetic species trees given a sample of gene trees under the coalescent model. It includes options to compute the ML species tree, search the space of all species trees for the k trees of highest likelihood and compute ML branch lengths for a user-input species tree.

AVAILABILITY:

The STEM package, including source code, is freely available at http://www.stat.osu.edu/~lkubatko/software/STEM/.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
19211573
[PubMed - indexed for MEDLINE]
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