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neighborjoining.jl

Julia package for the neighbor joining algorithm

https://github.com/benjamindoran/neighborjoining.jl

Science Score: 44.0%

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    Low similarity (8.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Julia package for the neighbor joining algorithm

Basic Info
  • Host: GitHub
  • Owner: BenjaminDoran
  • License: bsd-3-clause
  • Language: Julia
  • Default Branch: main
  • Size: 9.52 MB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 1
  • Open Issues: 1
  • Releases: 4
Created almost 3 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

NeighborJoining

Stable Dev Build Status Coverage

NeighborJoining

This package contains algorithms for neighbor joining

What is currently implemented?

  • regular Neighborjoining regNJ(): Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406-425 (1987).
  • fast NeighborJoining fastNJ(): Li, J. F. A fast neighbor joining method. Genet Mol Res 14, 87338743 (2015).
    • uses heuristics, will not always find the additive tree

Installation

add NeighborJoining

Examples

```

make distance matrix

d = rand(10, 10)^2 for i in 1:size(d,1) d[i,i]=0 end;

regular neighbor joining

njclusts = regNJ(d)

or fast neighbor joining

njclusts = fastNJ(d)

convert to newicktree string for export to other packages

nwstring = newickstring(njclusts)

adding labels to the leaves

labels = ["leaf $i" for i in 1:10] nwstring = newickstring(njclusts, labels)

adding labels to the internal nodes

nwstring = newickstring(njclusts, labels; labelinternalnodes=true) ```

Owner

  • Name: Benjamin Doran
  • Login: BenjaminDoran
  • Kind: user
  • Location: Chicago, IL
  • Company: UChicago

PhD Student - Computational Biology

Citation (CITATION.bib) 

@misc{NeighborJoining.jl,
	author  = {Benjamin Doran and collaborators},
	title   = {NeighborJoining.jl},
	url     = {https://github.com/BenjaminDoran/NeighborJoining.jl},
	version = {v0.1.0},
	year    = {2023},
	month   = {2}
}

GitHub Events

Total
  • Release event: 1
  • Issue comment event: 5
  • Push event: 3
  • Pull request event: 4
  • Fork event: 1
  • Create event: 2
Last Year
  • Release event: 1
  • Issue comment event: 5
  • Push event: 3
  • Pull request event: 4
  • Fork event: 1
  • Create event: 2