Journal Article

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

Laura S. Kubatko, Bryan C. Carstens and L. Lacey Knowles

in Bioinformatics

Volume 25, issue 7, pages 971-973
Published in print April 2009 | ISSN: 1367-4803
Published online February 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp079
STEM: species tree estimation using maximum likelihood for gene trees under coalescence

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Summary: 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/.

Contact: lkubatko@stat.osu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1721 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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