Announcing Phylogenetics

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Ben Ward

Jun 29, 2013, 7:39:31 PM6/29/13
For some time I've been playing with code that will read in Nexus trees and some types with which to represent trees. Julia has no package for Phylogenetics or evolution analyses of data, even though Biological Sequences are represented nicely by BioSeq. I've created the Phylogenetics.jl package/repository to work towards remedying this, and developed basic functions to read in the common Newick format file. Two types for representing trees are introduced and functions to read both out are also included. I am currently working on getting PhyloXML format data in and out and a more complex type to contain trees and more detailed data and information annotated along the trees. It is a work in progress and will build as I get around to implementing various features and others contribute their code and ideas. In it's infancy I've used ape as a mental springboard since I've used it extensively in mainline work (see the Phylo object implemented there), but I'm excited about the capabilities of Julia for parallel computing and the possibility of faster permutations - bootstrapping and ML/Bayes in Julia thanks to it's fast compiler and people working on it far better at more complex mathematics than I can hope to be. I'm sure then it will evolve as Julia's conventions, best practice, and exceptional features affect it, moving beyond it's initial similarities to ape. I'm also keen to ensure it is compatible with packages like BioSeq as it grows.  

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