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Tracking issue for phylogeny reconstruction algorithms #467

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RagnarGrootKoerkamp opened this issue Nov 25, 2021 · 0 comments
Open

Tracking issue for phylogeny reconstruction algorithms #467

RagnarGrootKoerkamp opened this issue Nov 25, 2021 · 0 comments

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@RagnarGrootKoerkamp
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I'm working on an implementation for the UPGMA and Neighbour Joining algorithms.

The plan is the following:

  • Update Tree type in rust-bio-types to be directed or undirected (NJ gives undirected output)
  • Add a DistanceMatrix type to rust-bio-types
  • Add parsers/fileIO methods for both Tree and DistanceMatrix, mapping to .phylip files (both strict and non-strict) and newick
  • Implement the UPGMA and Neighbour Joining algorithms in rust-bio.

For the parsing of the files, I'm planning to use nom, but I could also hand-write a parser.

Comments are welcome ;)
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