Software Made Available to the Public by Marc A. Suchard

The following is a list of programs available or that will be made available shortly. If you are interested in using any programs not currently available, please contact me directly via email.

File Name

File Size

Description

StepBrothers.tgz

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

MrBayesPlugin.zip

1.2MB

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

PR.tgz

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.

BAli-Phy.tgz

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

DualBrothers.tgz

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

HPM.tgz

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.

QMatrices.tgz

<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.

OhBrother-0.3.tgz

<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.