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  1. BeastLieMarkov BeastLieMarkov Public

    Beast 2 plugin implementing the distingished pair Lie Markov models of DNA evolution

    Java 2

  2. pal-mdw pal-mdw Public

    A modified version of the Phylogenetics Analysis Library (PAL, 1.5.1)

    Java

  3. mdwUtils mdwUtils Public

    Miscellaneous code I use in multiple projects, not dependent on third party libraries (such as PAL or BioJava)

    Java

  4. biojavaExtensions biojavaExtensions Public

    Reusable code extending the capabilities of Biojava 1.8.4. (Old version because I'm using Nexus parsing, which didn't make it to later Biojava versions.)

    Java

  5. pal-1.5.1 pal-1.5.1 Public

    Phylogenetics Applications Library, version 1.5.1. THIS IS NOT MY WORK.

    Java

  6. HybridSeq HybridSeq Public

    Simulates phylogeny with reticulation and produces sequences. Subsumed into the HybridSim program.

    Java 1