population genetic/genomics - tools

General Popgen 

• libsequence and related software

• BioPerl

• Genetic Analysis Software List

Analysis

Approximate Bayesian Computation

• DIYABC
• popABC
• msABC
• ABCreg etc.

Recombination and Gene Conversion

• Overpaint
• LDHat
• maxdip and maxhap

Simulation

Forward simulation

• Fregene
• SFS Code
• FPG
• EasyPop
• simuPop
• Bottlesim
• rmetasim
• kernelPop
• Nemo and Marlin
• ALF

Coalescent simulation

• ms and msHot
• MaCS
• SimCoal and a GUI
• Serial-SimCoal
• Genome
• cosi
• treevolve
• FastCoal
• CoaSim
• mlcoalsim
• COMPASS
• Splatche

Coalescent with selection

• Innan and Kim
• msms
• mssel
• SelSim
• Thornton and Jensen

Marker-specific simulation

• DAWG sequences with indels
• Seq-Gen sequences
• indel-Seq-Gen sequences with indels
• microsat microsatellites