StepBrothers is implementation of the Random Tips model. It is a descendant of the DualBrothers model developed by Minin et. al. The random tips model adopts the use of a single phylogenetic tree with a random number of tips rather than multiple trees at different time points. Its advantages include more plausible assumptions regarding the evolutionary process and joint analyses of recombinants. The random tips model also allows dating information to be obtained.
Marc A. Suchard, M.D., Ph.D.
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Bloomquist EW, Dorman KS, Suchard MA.
StepBrothers: inferring partially shared ancestries among recombinant viral sequences.
Biostatistics. 2009 Jan;10(1):106-20.