Modiphy is a project mainly written in Scala, based on the MIT license.
Flexible Scala Library for hypothesis testing using phylogenetic models
Library for phylogenetic analysis using Scala.
Because I want to be able to rapidly develop evolutionary models and test them. Scala is fast (enough) to run, fast to develop, and has threadless parallelism with Actors.
Currently this software is in the testing phase. Documentation is sparse.
I want to include HMM-based models (i.e. tree-HMM or phylo-HMM type features). I would like to develop this into a full domain specific language. It hasn't had any optimisation yet.
Modiphy is licensed under the MIT/X license.
Dependencies:
You need Simple Build Tool Dependencies should be automatically handled by SBT. You also need Apache Ivy in the classpath for SBT:
sbt update # to pull in latest jars
sbt compile