Other programs for Bayesian estimation of phylogeny:
A nice program by Bret Larget and Donald Simon for the Bayesian inference
A program by Paul-Michael Agapow that deals with gaps as a
fifth state. This link is temporary disabled?
BEAST, written by Alexei Drummond and Andrew Rambaut, is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is particularly good for molecular clock analyses.
Paul Higgs is the author of Phase, designed specifically for use with RNA sequences that have a conserved secondary structure, e.g. rRNA and tRNA.
Tools for use with MrBayes:
A program by Johan Nylander for selecting DNA substitution models.
Programs for the maximum likelihood estimation of phylogeny:
David Swofford's program implements the maximum likelihood method
under a number of nucleotide models.
Ziheng Yang's program implements virtually every model of
molecular evolution that has been proposed. (This is not
surprising as he invented many of them.)
Joe Felsenstein's package of programs includes one of the earliest
implementations of likelihood-based estimation of phylogeny. Incidentally, Felsenstein
was also an early proponent of Bayesian estimation of phylogeny: Just
read his 1968 Ph.D. Thesis!
A program by Jun Adachi and Masami Hasagewa that for a long time was the
only game in town for maximum likelihood estimation of phylogeny using
amino acid sequences.
A program by Pietro Lio that implements several models of amino acid
change, including several Hidden Markov Models that can be used to
predict secondary structure.
Other phylogeny programs:
- An extensive list of phylogeny programs is available from