:: DESCRIPTION
BANANAS is a software for inferring population trees based on molecular marker data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Siren, J., Marttinen, P. and Corander, J. 2011.
Reconstructing Population Histories from Single Nucleotide Polymorphism Data.
Molecular Biology and Evolution. 28:673-683.
:: DESCRIPTION
StepBrothers is implementation of the Random Tips model. It is a descendant of the DualBrothers model developed by Minin et. al. The random tips model adopts the use of a single phylogenetic tree with a random number of tips rather than multiple trees at different time points. Its advantages include more plausible assumptions regarding the evolutionary process and joint analyses of recombinants. The random tips model also allows dating information to be obtained.
::DEVELOPER
Marc A. Suchard, M.D., Ph.D.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bloomquist EW, Dorman KS, Suchard MA.
StepBrothers: inferring partially shared ancestries among recombinant viral sequences.
Biostatistics. 2009 Jan;10(1):106-20.
:: DESCRIPTION
METREE is intended to find the minimum evolution (ME) tree that has the smallest value of the sum of branch lengths (S) for a set of sequences, identify a set of trees whose S are not significantly different from that of the ME tree, and print out the resulting trees in a publishable form. The branch lengths for each topology are estimated by the ordinary least-squares method from a matrix of evolutionary distances.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Comput Appl Biosci. 1994 Jul;10(4):409-12.
METREE: a program package for inferring and testing minimum-evolution trees.
Rzhetsky A, Nei M.
:: DESCRIPTION
PopABC (Approximate Bayesian computation) is a computer package to estimate historical demographic parameters of closely related species/populations (e.g. population size, migration rate, mutation rate, recombination rate, splitting events) within a Isolation with migration model. The software performs coalescent simulation in the framework of approximate Bayesian computation (ABC, Beaumont et al, 2002). PopABC can also be used to perform Bayesian model choice to discriminate between different demographic scenarios.
::DEVELOPER
Joao Lopes and Mark Beaumont
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PopABC: a program to infer historical demographic parameters
Joao S. Lopes, David Balding and Mark A. Beaumont1
Bioinformatics (2009) 25 (20): 2747-2749.
:: DESCRIPTION
CryoBayes is a Bayesian method for inferring 3D structure of macromolecules imaged by Electron Cryo-Microscopy experiments. We encourage experimental Structural Biologists to download and try our code. We hope that our technique will be useful as a method of automatically generating intial models given only class average images.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Jaitly, N., Brubaker, M.A., Rubinstein, J.L. and Lilien, R.H.
A Bayesian Method for 3-D Macromolecular Structure Inference using Class Average Images from Single Particle Electron Microscopy,
Bioinformatics, 26(19):2406-15 (2010).
:: DESCRIPTION
Structurama is a program for inferring population structure from genetic data. The program assumes that the sampled loci are in linkage equilibrium and that the allele frequencies for each population are drawn from a Dirichlet probability distribution. The method implements two different models for population structure. First, Structurama implements the method of Pritchard et al. (2000) in which the number of populations is considered fixed. The program also allows the number of populations to be a random variable following a Dirichlet process prior (Pella and Masuda, 2006; Huelsenbeck and Andolfatto, 2007).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
John P. Huelsenbeck, Peter Andolfatto, and Edna T. Huelsenbeck
Structurama: Bayesian inference of population structure
Evol Bioinform Online. 2011; 7: 55–59.
:: DESCRIPTION
PhySIC_IST aims at inferring supertrees that satisfy the same appealing theoretical properties as with PhySIC, while being as informative as possible under this constraint.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
“PhySIC_IST: cleaning source trees to infer more informative supertrees.”
Scornavacca C., Berry V., Lefort V., Douzery E.J.P. and Ranwez V.
BMC Bioinformatics. 2008, Oct 4;9:413
:: DESCRIPTION
The AIRnet project provides an open-source tool for inferring Gene Regulatory Networks from correlations between gene activation state changes. AIRnet uses microarray data and can read SOFT formatted family files, DataSet SOFT files, as well as other tab-separated formats.
::DEVELOPER
Computational Science Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Inferring gene regulatory networks from asynchronous microarray data with AIRnet.
Oviatt D, Clement M, Snell Q, Sundberg K, Lai CW, Allen J, Roper R.
BMC Genomics. 2010 Nov 2;11 Suppl 2:S6.
:: DESCRIPTION
Margarita infers genealogies from population genotype data and uses these to map disease loci.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mapping trait loci by use of inferred ancestral recombination graphs.
Minichiello MJ and Durbin R
American journal of human genetics2006;79;5;910-22
