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Collection of executable jarfiles for a variety of tasks.

Generally compatible with Java 1.6+.

Hint: you'll need to right-click on the compressed archives and choose 'Save link as...' in most browsers...


While some elements of this code have test harnesses and been written to test specifications, the vast majority of methods have only undergone limited testing.

You should use this code at your own risk and in particular, compare to your expectations and other applications' output.

If you think you have found a bug, please report it here: https://github.com/lonelyjoeparker/qmul-genome-convergence-pipeline/issues


If you have a problem or need help using a binary, please first read this general release information. If you think you have found a bug or error please check the existing issues on GitHub. If you still haven't got any further and want to send a question, email joe+bioinformaticshelp@kitserve.org.uk. I may or may not be able to answer your question quickly. Please include these details:

  • Which Java version, and which jarfile you are using (and where/when you downloaded it);
  • Which OS and version you're using;
  • Error trace from the console (this will usually have the word 'Exception:' and some other lines, probably numbered);
  • The input command and input files as well as any output. If your input/output files are larger than 1MB, please either send only the first few lines, or else use an online filestore like http://wetransfer.com to send me the whole input.


For usage details and examples, see the specific READMEs:

  • CONTEXT (the COmparativeNucleotide(and)TreesExplorationTool; previously 'PhylogenomicDatasetBrowser'): CONTEXT.md
    • GUI application to browse and rapidly sort/compare phylogenomic-scale datasets (thousands of alignments/phylogenies).
  • SimpleMRCASubstitutionDetector: README_SimpleMRCASubstitutionDetector.md
    • Reconstructs ancestral sequences using parsimony, finds and prints parallel substitutions
  • BasicAlignmentStats: no readme available yet
    • Reads an alignment or directory of alignments and prints descriptive statistics (length, gappiness, entropy etc) for each one.
  • GeneralConvergenceApplicationGUI: no readme available yet
    • GUI application to create and run convergence detection analyses on phylogenomic data. Not released.

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)
  • XChart - XChart chart/plotting library by Tim Molter v3.3.1 (XChart-3.3.1.jar)

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