feat: Add UPGMA, Neighbor-Joining, and Robinson-Foulds metric #470
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This adds the `to_string`, `to_file`, and `write` methods to `newick.rs`, mirroring the existing `from_string`, `from_file` and `read` methods. A slight annoyance is that petgraph iterates outgoing edges in reverse order of adding them. To keep input and output consistent, I manually reverse that order back to the natural order in which they were added. Another option would be to actually add them in the reverse order, but that would change the representation which may not be desirable. I'm also changing the `"N/A"` value for nodes without a name to just the empty string as this heavily pollutes the `to_string` representation, and `""` is more naturaly IMO. Also fixed one unused variable warning.
This mirrors `newick.rs` and adds string/file IO for the `bio_types::distancematrix::DistanceMatrix` type, in the Phylip distance matrix format. It supports square and (upper/lower) triangular matrices. Triangular matrices must not contain the diagonal. Also fix a broken doctest.
Instead, loop over all vertices to find it, and return an error if the root is not unique.
This adds implementations of phylogeny reconstruction algorithms and the Robinson-Foulds metric to compute distances between two phylogenetic trees.
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This depends on #468 and #469.
It adds implementations of the UPGMA and Neighbor-Joining phylogeny reconstruction algorithms, and of the Robinson-Foulds metric used as a distance between two trees.