Coalescent Theory Calculation Software on the NetBeans Platform
By Geertjan-Oracle on May 22, 2013
Coalescent is an open source tool in coalescent theory.
It provides solutions for the exact calculation of likelihood under infinite sites and infinite alleles models of mutations in population genetics.
Additionally, it checks phylogeny and draws gene trees for infinite sites data.
Planned features for the upcoming releases will focus on the following areas:
- Importance sampling under infinite sites model.
- MCMC under infinite sites model model.
- Exact calculation with infinite sites/alleles and various migration models.
- Exact calculation with infinite sites/infinite alleles and discrete recombination models.
- Sampling algorithms for migration and recombination.
- Fine-scale recombinations, such as LDHat/LDHelmet.