1.6MB

Java implementation of the random tips model and posterior sampler from:
Bloomquist EW, Dorman KS, Suchard MA (submitted) The (evil) stepbrothers: inferring partially shared ancestries among recombinant viral sequences, Biostatistics.
CLICK HERE

1.2MB

Geneious v2.5.4 (or above) plug-in to perform and analyze simple Bayesian phylogenetic reconstruction.

0.1MB

WinBUGS implementation of phylogenetic repeated measures models described in:
Guo H, Weiss RE, Gu X, Suchard MA (in press) TimeSquared: repeated measures on phylogenies, Molecular Biology and Evolution.

0.5MB

BAliPhy -- Bayesian Alignment and Phylogeny.
Details found in:
Redelings BD, Suchard MA (2005) Joint Bayesian estimation of alignment and phylogeny, Systematic Biology.
Markov chain Monte Carlo sampler written in C++ to simultaneously explore the joint posterior distribution of alignment and phylogeny.
CLICK HERE

0.5MB

Java implementation of the dual multiple change-point sampler from:
Minin V, Dorman KS,Fang F, Suchard MA (2005) Dual multple change-point model leads to more accurate recombination detection, Bioinformatics.
CLICK HERE

0.3MB

Java implementation of the hierarchical phylogenetic model used in:
Kitchen CMR, Philpott S, Burger H, Weiser B, Anastos K, Suchard MA (revised) Evolution of HIV-1 coreceptor usage during antiretroviral therapy: a Bayesian approach, Journal of Virology.
Contact Marc Suchard via email for downloading instructions.

<0.1MB

Java implementation of the continuous time Markov chain evolutionary models used in:
Suchard MA, Weiss RE, Sinsheimer JS (2003) Testing a molecular clock without an outgroup: derivations of induced priors on branch length restrictions in a Bayesian framework, Systematic Biology, 52:48-54.
Contains both reversible and irreversible models, most noteably SSL98.

<0.1MB

Java implementation of the Bayesian multiple change-point model used in:
Suchard MA, Weiss RE, Dorman KS, Sinsheimer JS (2002) Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage, Systematic Biology 51:715-728.
Program estimates regional heterogeneity in the substitution process and can be used to infer recombination.