SLiM

SLiM (Selection on Linked Mutations) is a forward population genetic simulation for studying linkage effects such as hitchhiking under recurrent selective sweeps, background selection, and Hill-Robertson interference. The program can incorporate complex scenarios of demography and population substructure, various models for selection and dominance of new mutations, realistic gene and chromosome structure, and user-defined recombination maps. Special emphasis was further placed on the ability to model and track individual selective sweeps - both complete and partial. While retaining all capabilities of a forward simulation, SLiM utilizes sophisticated algorithms and optimized data structures that enable simulations on the scale of entire eukaryotic chromosomes in reasonably large populations. All these features are implemented in an easy-to-use C++ command line program.
Description: http://www.stanford.edu/%7Emesser/img/introgression.jpg
Example of an evolutionary scenario that can be modeled with SLiM (example 4 in the documentation): The scenario features a population split with subsequent bottleneck, followed by the introgression of an adaptive mutation from the source population into the new subpopulation.

SLiM was designed and implemented by Philipp Messer.

Documentation can be found here.

Code can be found here.

 

Drosophila melanogaster Recombination Rate Calculator

This web tool allows you to estimate rates of recombination anywhere in the Drosophila melanogaster genome. This recombination rate calculator is fast, and is tailored to your specific request. Please pick the release of the D. melanogaster genome you would like to use. Also, choose whether you would like to perform a query for a single locus or for multiple loci. Drosophila melanogaster recombination rate calculator is available here.

Forward Reverse Test, version 2.0

This is a test of mutational constancy based on the comparison of forward and reverse rates of nucleotide substitution. Under the assumption that mutation rates are constant between two classes of genomic sequences, one can calculate the strength of fixational bias that underlies the variability in forward and reverse substitution rates. When fixation biases thus inferred are too strong, the mutation rates must vary along with the substitution rates. This web application was designed and implemented by Peter Arndt, Misha Lipatov and Dmitri Petrov (Lipatov et al., 2006).

PGEToolbox: Matlab Toolbox for Population Genetics and Evolution

imagePGEToolbox is a Matlab-based software package for analysis of polymorphism and divergence data for population genetics and evolution. It estimates several basic statistics of DNA sequence variation and carries out statistical tests of selective neutrality under the infinite alleles model, such as Tajima's D test, Fu & Li's tests and Fay & Wu's H test. The significance of tests is determined from the distribution of the statistics obtained by coalescent simulation. The toolbox performs McDonald-Kreitman test (and several extensions). PGEToolbox also contains functions for handling SNP (Single Nucleotide Polymorphism) genotype data. PGEToolbox is open-sourced, can be easily extended or tailored for specific tasks, and scaled up for large data sets.For academic uses, PGEToolbox is available free of charge at http://bioinformatics.org/pgetoolbox/.

MBEToolbox: Matlab Toolbox for Molecular Biology and Evolution

imageMatlab is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in Matlab to perform the sequence data analyses specifically required for molecular biology and evolution. We have developed a Matlab toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned Matlab users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://bioinformatics.org/mbetoolbox/.