josiahseaman / qmul-genome-convergence-pipeline

API and binaries for phylogenomic analyses, particularly comparison of input trees/alignments (CONTEXT) and detecting genomic convergence

qmul-genome-convergence-pipeline

Automatically exported from code.google.com/p/qmul-genome-convergence-pipeline

A collection of Java libraries and executables for conducting phylogenomic analyses, mainly for convergence detection. Includes wrappers to a variety of tools including PAML, RAxML, and PhyloBayes.

Projects:

Several projects including:

• CONTEXT, a phylogenomic dataset browser (current major version: v0.8.prerelease)(all versions)
• A simple MRCA substitution detector for finding parallel substitutions given an alignment and phylogeny (current: public alpha, no version number)
• A genome convergence detection pipeline (current: in progress - no public release)

Depdendencies and packaged libraries

Requires Java 1.6+. The codebase references the following open-source libraries:

• Colt - Open Source Libraries for High Performance Scientific and Technical Computing (colt.jar)
• JAMA - Java Matrix Algebra (1.0.3, 2012.11.09; Jama-1.0.3.jar)
• JSC - Java Statistical Classes v1.0 (jsc-1.jar)
• XStream - Java XML bindings (xstream-1.4.4.jar and dependencies)
• JFreeChart (jfreechart-1.0.14.jar)
• JEBL - Java Evolutionary Biology Library v0.4 (jebl-0.4.jar)

The executable jarfiles (see trunk/bin directory) come with these build-path dependencies already packaged. They should run as standalone Java apps with no additional dependencies