ALIFRITZ performs statistical multiple alignment and phylogeny reconstruction simultaneously. It implements a strategy based on simulated annealing which makes use of these models to infer a phylogenetic tree for a set of DNA or protein sequences together with the sequences’ indel history, i.e. their multiple alignment augmented with information about the positioning of insertion and deletion events in the tree.
:: MORE INFORMATION
Roland Fleißner, Dirk Metzler and Arndt von Haeseler,
Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction.
Syst. Biol., 54, 548-561