neighborjoining.jl - v0.2.1

NeighborJoining v0.2.1

Diff since v0.2.0

merged PR #4 adding an order function to aid with plotting the NJClust object

Merged pull requests: - feat: add order function (#4) (@cvigilv) - bump version to 0.2.1 (#5) (@BenjaminDoran)

- Julia
Published by github-actions[bot] 8 months ago

neighborjoining.jl - v0.2.0

NeighborJoining v0.2.0

Diff since v0.1.2

Dev (v0.2) rewrite

Revise regNJ function:

It now only uses the memory space of a single distance matrix, and overwrites new nodes into one of the merged nodes. This does change the ordering of merges in the algorithm (i.e. the pseudoroot may change) but the unrooted tree is confirmed to be the same (i.e. patristic distances don't change).

Update testing framework:

followed SciML organization with safetestsets and made each testset a regular script

Update Docs:

added doctests, and new docstrings for heights and merges functions

Add benchmark suite:

I am now testing on matrices up to size 1024, with the revision regNJ seems much faster than before, but some of that seems to be testing on yuletree matrices rather than uniformly random matrices

Merged pull requests: - Dev (v0.2) rewrite (#3) (@BenjaminDoran)

- Julia
Published by github-actions[bot] about 2 years ago

neighborjoining.jl - v0.1.2

update install documentation

Full Changelog: https://github.com/BenjaminDoran/NeighborJoining.jl/compare/v0.1.1...v0.1.2

- Julia
Published by BenjaminDoran over 2 years ago

neighborjoining.jl - v0.1.1

Initial release

Implements:

• regular neighbor joining
• fast neighbor joining

- Julia
Published by BenjaminDoran over 2 years ago