Monophyler computes the probability of monophyly of a specified set of gene lineages conditional on a species tree. Monophyler uses the coalescent together with an arbitrary species tree to determine the monophyly probability for a set of lineages or the reciprocal monophyly probability for a pair of sets of lineages. It can also accommodate various computations involving three or four lineage sets.
Rosenberg lab at Stanford University
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Mehta RS, Bryant D, Rosenberg NA.
The probability of monophyly of a sample of gene lineages on a species tree.
Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):8002-9. doi: 10.1073/pnas.1601074113. Epub 2016 Jul 18. PMID: 27432988; PMCID: PMC4961160.