Crate phylogeny

This library provides algorithms and helper functions for constructing and comparing phylogenies.

Currently, it contains these datatypes:

• DistanceMatrix, representing a .phylip square symmetric distance matrix.
• Phylogeny, representing a .newick file phylogeny.

And it contains these algorithms:

• UPGMA, a phylogeny reconstruction method.
• Neighbor-Joining, another phylogeny reconstruction method.
• Robinson-Foulds metrid, a distance metric between phylogenies.

There is an accompanying binary rpt to call these algorithms from the command line. Run cargo install phylogeny followed by rpt --help for more details.

Structs

DistanceMatrix

A symmetric square matrix representing a .phylip file.

Phylogeny

A phylogeny representing a .newick file.

Functions

neighbor_joining

Run the Neighbor-Joining algorithm

robinson_foulds_distance

Compute the Robingson-Foulds metric.

upgma

Run the UPGMA algorithm.

Type Definitions

Result

A convenience result type.