Wednesday May 22, 2013

Coalescent Theory Calculation Software on the NetBeans Platform

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:

  1. Importance sampling under infinite sites model.
  2. MCMC under infinite sites model model.
  3. Exact calculation with infinite sites/alleles and various migration models.
  4. Exact calculation with infinite sites/infinite alleles and discrete recombination models.
  5. Sampling algorithms for migration and recombination.
  6. Fine-scale recombinations, such as LDHat/LDHelmet.

More info:


Geertjan Wielenga (@geertjanw) is a Principal Product Manager in the Oracle Developer Tools group living & working in Amsterdam. He is a Java technology enthusiast, evangelist, trainer, speaker, and writer. He blogs here daily.

The focus of this blog is mostly on NetBeans (a development tool primarily for Java programmers), with an occasional reference to NetBeans, and sometimes diverging to topics relating to NetBeans. And then there are days when NetBeans is mentioned, just for a change.


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