-
Notifications
You must be signed in to change notification settings - Fork 10
Home
Lars Arvestad edited this page Apr 9, 2015
·
8 revisions
JPrIME is a Java library with tools for phylogenetics. PrIME and JPrIME have an emphasis on probabilistic phylogenetic models that typically employ a Markov-chain Monte Carlo (MCMC) framework. It is a complement to the the original C++ library PrIME developed by people in computational biology at KTH and Stockholm University.
- Using the DLRS model -- A tutorial on how to work with the Duplication/Loss model.
- Using the DLTRS model -- A tutorial on how to work with the Duplication/Loss/Transfer model.
- GenPhyloData Tutorial -- Learn how to generate synthetic phylogenies and reconciled phylogenies. And hybridisation networks!
For the advanced users, there is:
- a developers guide
- and instructions for how to create releases.
The project was started by Jens Lagergren, Lars Arvestad and Bengt Sennblad.
Large parts of JPrIME can be attributed to Joel Sjöstrand. More recent contributors are Mehmood Alam Khan, Owais Mahmudi, Ikram Ullah, Raja Hashim Ali, and Sayyed Auwn Muhammad.
Most of this manual have been written by Joel Sjöstrand, with some edits by Lars Arvestad.