Bioinformatics · 2009 · 485 citations · 20 references
Life SciencesBioinformaticsEvolutionary BiologyEvolutionary TheoryPhylogeneticsSequence AnalysisCoalescent-based PhylogeneticsGene Tree InferenceMaximum Likelihood PhylogeneticsPhylogenetic AnalysisPhylogenetic Tree ReconstructionSpecies Tree InferenceCoalescent-based Species Tree EstimationCoalescent-based Species TreesMaximum Likelihood Estimation AlgorithmsMaximum Likelihood Gene Tree InferenceMaximum Likelihood InferenceMaximum Likelihood PhylogenyMaximum Likelihood Species Tree InferenceMaximum Likelihood Tree Search
UNLABELLED: 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.
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