:: DESCRIPTION
BayesDiallel is a Gibbs-sampler program designed to fit, image, and give confidence for intricately modeled inheritance in Diallel F1 cross data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lenaric A, Svenson K, Churchill G, Valdar W, (2012)
A General Bayesian Approach to analyzing Diallel Crosses of Infred Strains
Genetics, Vol. 190, 413-435, February 2012.
:: DESCRIPTION
MIMAR (MCMC estimation of the Isolation-Migration model Allowing for Recombination) is a Markov chain Monte Carlo method to estimate parameters of an isolation-migration model. It uses summaries of polymorphism data at multiple loci surveyed in a pair of diverging populations or closely related species and in contrast to previous methods, allows for intralocus recombination. Note that you need to know the ancestral allele at each polymorphic site in order to calculate the summary statistics.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Becquet and Przewroski (2007)
A new approach to estimate parameters of speciation models with application to apes
Genome Res. 2007. 17: 000
:: DESCRIPTION
SwiftLink performs multipoint parametric linkage analysis on large consanguineous pedigrees and is primarily targeted at pedigrees that cannot be analysed by a Lander-Green algorithm based program, i.e. many markers, but larger pedigrees.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2013 Feb 15;29(4):413-9. doi: 10.1093/bioinformatics/bts704. Epub 2012 Dec 13.
SwiftLink: parallel MCMC linkage analysis using multicore CPU and GPU.
Medlar A1, Głowacka D, Stanescu H, Bryson K, Kleta R.
:: DESCRIPTION
SGD is a software for parameter inference in discretely observed stochastic kinetic models
::DEVELOPER
CBCL Lab (Computational Biology and Computational Learning) @ UCI
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Yuanfeng Wang, Scott Christley, Eric Mjolsness and Xiaohui Xie,
Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent
BMC Systems Biology 2010, 4:99 doi:10.1186/1752-0509-4-99.
:: DESCRIPTION
RPMCMC is a parallel MCMC algorithm for discovering diverse motifs from large sequence sets
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets.
Ikebata H, Yoshida R.
Bioinformatics. 2015 Jan 11. pii: btv017
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
BayesPhylogenies is a general package for inferring phylogenetic trees using Bayesian Markov Chain Monte Carlo (MCMC) or Metropolis-coupled Markov chain Monte Carlo (MCMCMC) methods. The program allows a range of models of gene sequence evolution, models for morphological traits, models for rooted trees, gamma and beta distributed rate-heterogeneity, and implements a ‘mixture model’ (Pagel and Meade, 2004) that allows the user to fit more than one model of sequence evolution, without partitioning the data.
::DEVELOPER
Reading Evolutionary Biology Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data.
Pagel M, Meade A.
Syst Biol. 2004 Aug;53(4):571-81.
:: DESCRIPTION
iMCMC is a Macintosh application that illustrates Markov chain Monte Carlo (MCMC) for a simple landscape.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MCMC++ is a class library intended to speed and simplify development of Markov Chain Monte Carlo models for analysis of data in a Bayesian context.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. Annotates the locations of conserved elements in multiple sequence while correcting for alignment uncertainty and error.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Evol Biol. 2009 Aug 28;9:217.
BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.
Satija R, Novák A, Miklós I, Lyngs? R, Hein J.
