Leaphy 1.0 beta
Leaphy (Likelihood Estimation Algorithms in Phylogenetics) uses maximum likelihood (ML) to estimate trees from aligned amino acid and nucleotide sequences under a variety of commonly used and popular models.
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New approaches to phylogenetic tree search and their application to large numbers of protein alignments.
Syst Biol (2007) 56 (5): 727-740. doi: 10.1080/10635150701611134