A growing collection of tools used in evolutionary research. From analytical methods over helpful code and webservices to ready-to-use programs.
There is an incredibly wide variety of tools that are helpful for evolutionary research, so it is almost impossible to maintain a good overview. Nevertheless it is handy to have some frequently used links listed here. If you want your favourite tool to be listed, let us know.
DNA Sequence Analysis
- DNAsp: "'DNA Sequence Polymorphism' is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data."
- MEGA: "'Molecular Evolutionary Genetics Analysis' is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses."
- Arlequin3: An integrated software for population genetics data analysis that includes various intra-population and inter-population methods (several neutrality tests, mismatch distributions, Fst and many other statistics).
- SimCoal2: "A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models." Very userfriendly. Provides output in Arlequin format.
- CoaSim: "CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models." Very flexible if you are willing to program in various languages.
Evolution: Other helpful link collections
- Joe Felsenstein's List of Phylogeny Programs: Possibly the most comprehensive list of programs in use for analyzing evolution
Mathematics & Statistics
- Mathematica (Encyclopedia: Mathworld - online version for simple tasks: QuickMath)
- R Statistical Computing programming language
- StatSoft Textbook: Statistics Methods and Applications
- Google code: Search publicly available source code