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.
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.
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.
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.
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).
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.
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.