Skip to content

lonelyjoeparker/qmul-genome-convergence-pipeline

master
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.

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:

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

About

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

Topics

Resources

Stars

Watchers

Forks

Packages

No packages published