Tracer 1.7.1 – Analyse Results from Bayesian MCMC programs such as BEAST & MrBayes

Tracer 1.7.1

:: DESCRIPTION

Tracer is a program for analysing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain). It can be used to analyse runs of BEAST, MrBayes, LAMARC and possibly other MCMC programs.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

Tracer

:: MORE INFORMATION

Citation

Syst Biol. 2018 Sep 1;67(5):901-904. doi: 10.1093/sysbio/syy032.
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.
Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA.

MrBayes 3.2.7a – Bayesian Inference of Phylogeny

MrBayes 3.2.7a

:: DESCRIPTION

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes’s theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

::DEVELOPER

MrBayes Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

MrBayes

:: MORE INFORMATION

Citation:

MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP.
Syst Biol. 2012 May;61(3):539-42. doi: 10.1093/sysbio/sys029.

Ronquist F, Huelsenbeck JP.
MrBayes 3: Bayesian phylogenetic inference under mixed models.
Bioinformatics. 2003 Aug 12;19(12):1572-4.

GPU MrBayes 3.1 – MrBayes on a Graphics Processing Unit

GPU MrBayes 3.1

:: DESCRIPTION

GPU MrBayes is a modified version of MrBayes that enables running Metropolis coupled  Markov  chain Monte Carlo (MC)^3 sampling on a Graphics Processing Unit (GPU).

::DEVELOPER

Nankai-Baidu Joint Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GPU

:: DOWNLOAD

 GPU MrBayes

:: MORE INFORMATION

Citation:

GPU MrBayes V3.1: MrBayes on graphics processing units for protein sequence data.
Pang S, Stones RJ, Ren MM, Liu XG, Wang G, Xia H, Wu HY, Liu Y, Xie Q.
Mol Biol Evol. 2015 May 26. pii: msv129.

Bioinformatics. 2011 May 1;27(9):1255-61. doi: 10.1093/bioinformatics/btr140. Epub 2011 Mar 16.
MrBayes on a graphics processing unit.
Zhou J1, Liu X, Stones DS, Xie Q, Wang G.

siMBa 1.0 – A simple GUI for MrBayes.

siMBa 1.0

:: DESCRIPTION

siMBa (simple MrBayes) is a graphical user interface for the phylogenetic analysis software, MrBayes.

::DEVELOPER

Thines Lab.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

 siMBa

:: MORE INFORMATION

Citation:

Mishra B, Thines M (2014)
siMBa — a simple graphical user interface for the Bayesian phylogenetic inference program MrBayes.
Mycological Progress 13:1255–1258

Burntrees 0.2.2 – Perl script for manipulating MrBayes tree and Parameter files

Burntrees  0.2.2

:: DESCRIPTION

Burntrees is a script for manipulating tree (*.t, *.trprobs, *.con) and parameter (*.p) files from MrBayes (v.3). The script exctracts trees and (by default) the taxon translation table and the trailing “end;” from a MrBayes tree file.

::DEVELOPER

Johan Nylander 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

 Burntrees

:: MORE INFORMATION