Algorithms for MDC-based multi-locus phylogeny inference
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
The deep coalescence consensus tree problem is Pareto on clusters
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
A self-adaptive computing framework for parallel maximum likelihood evaluation
The Journal of Supercomputing
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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.