erate is an extension of Joe Felsenstein’s DNAML program which treats insertions and deletions as evolutionary events, rather than ignoring them as missing data (which is what the most widely used phylogenetic inference programs all do).
Elena Rivas, Eddy lab
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Probabilistic Phylogenetic Inference with Insertions and Deletions.
E. Rivas, S. R. Eddy.
PLoS Comput. Biol., 4:e1000172, 2008.