- Open BEAGLE
- Open BEAGLE is an evolutionary computation framework. It provides an Object-Oriented software environment enabling the implementation of almost any kind of evolutionary algorithm, such as genetic algorithms and genetic programming. The only necessary condition is to have a population of individuals to which a sequence of evolving operations is iteratively applied. So far, two specialized frameworks have been implemented: genetic algorithms and genetic programming. An evolution strategies framework is also planned for a future release.
- PrIME (Probabilistic Integrated Models of Evolution) is a package supporting inference of evolutionary parameters in a Bayesian framework using Markov chain Monte Carlo simulation. A distinguishing feature of PrIME is that the species tree is taken into account when analyzing gene trees. The input data to PrIME is a multiple sequence alignment in FASTA format and the output data contains trees in Newick format.
- Primer Pooler
- This is a program for cancer researchers and others who want to use Multiplex PCR (polymerase chain reaction) to study DNA samples, and wish to optimize their combinations of primers. It can handle thousands of primers without being slow, and can also handle degenerate primers and automatically check for overlaps.
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