|
|
Links
Other programs for Bayesian estimation of phylogeny:
- BAMBE
A nice program by Bret Larget and Donald Simon for the Bayesian inference
of phylogeny.
- Mac5
A program by Paul-Michael Agapow that deals with gaps as a
fifth state. This link is temporary disabled?
- Beast
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.
- PHASE
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:
- MrModeltest2
A program by Johan Nylander for selecting DNA substitution models.
Programs for the maximum likelihood estimation of phylogeny:
- PAUP*
David Swofford's program implements the maximum likelihood method
under a number of nucleotide models.
- PAML
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.)
- PHYLIP
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!
- MOLPHY
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.
-
PASSML
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
Joe Felsenstein
here.
|
|
