https://github.com/banhbio/metaphylo.jl

Phylogenetic trees with metadata by Julia based on Graphs.jl and AbstractTrees.jl.
https://github.com/banhbio/metaphylo.jl

biodiversity bioinformatics julia phylogeny

Last synced: 4 months ago
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Phylogenetic trees with metadata by Julia based on Graphs.jl and AbstractTrees.jl.

• Host: GitHub
• URL: https://github.com/banhbio/metaphylo.jl
• Owner: banhbio
• License: mit
• Created: 2023-01-11T02:32:36.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-01-22T02:41:23.000Z (over 2 years ago)
• Last Synced: 2025-06-12T15:09:28.813Z (4 months ago)
• Topics: biodiversity, bioinformatics, julia, phylogeny
• Language: Julia
• Homepage:
• Size: 240 KB
• Stars: 4
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# MetaPhylo

[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://banhbio.github.io/MetaPhylo.jl/stable/)

[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://banhbio.github.io/MetaPhylo.jl/dev/)

[![Build Status](https://github.com/banhbio/MetaPhylo.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/banhbio/MetaPhylo.jl/actions/workflows/CI.yml?query=branch%3Amain)

[![Coverage](https://codecov.io/gh/banhbio/MetaPhylo.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/banhbio/MetaPhylo.jl)

[![DOI](https://zenodo.org/badge/587552550.svg)](https://zenodo.org/badge/latestdoi/587552550)

`MetaPhylo.jl` is Julia package for dealing with phylogenetic trees.

This package is in the early stage of development and probably has many bugs (especially around Newick format). Bug reports and any suggestions are welcome🙂!

## Acknowledgements

`MetaPhylo.jl` is inspired by [MetaGraphs.jl](https://github.com/JuliaGraphs/MetaGraphs.jl) and implemented with [Graphs.jl](https://github.com/JuliaGraphs/Graphs.jl) and [AbstractTrees.jl](https://github.com/JuliaCollections/AbstractTrees.jl).

## Example

```julia

julia> import Pkg; Pkg.add("MetaPhylo");

julia> using MetaPhylo

julia> tree = parse_newick("((A:0.1,B:0.2)100:0.3,((C:0.4,D:0.5)77:0.6,E:0.7)98:0.8,F:0.9);", MetaPhylo.Tree{Int, UnRooted, ReRootable})

MetaPhylo.Tree with 6 leaves.

    Rooted: false

    Rerootable: true

julia> print_tree(tree)

1: [root] 

├─ 2: [value:100.0, length:0.3] 

│  ├─ 3: [length:0.1] label:"A"

│  └─ 4: [length:0.2] label:"B"

├─ 5: [value:98.0, length:0.8] 

│  ├─ 6: [value:77.0, length:0.6] 

│  │  ├─ 7: [length:0.4] label:"C"

│  │  └─ 8: [length:0.5] label:"D"

│  └─ 9: [length:0.7] label:"E"

└─ 10: [length:0.9] label:"F"

julia> tree[3]

Dict{Symbol, Any} with 1 entry:

  :label => "A"

julia> tree[5,6]

Dict{Symbol, Any} with 2 entries:

  :value  => 77.0

  :length => 0.6

julia> findnodes(tree, :label => isequal("A"))

1-element Vector{Int64}:

 3

julia> findbranches(tree, :value => x -> x ≥ 90)

1-element Vector{Graphs.SimpleGraphs.SimpleEdge{Int64}}:

 Edge 1 => 2

 Edge 1 => 5

julia> @time big_tree = Newick.File("/path/to/big_tree") |> MetaPhylo.Tree{Int, UnRooted, ReRootable}

  3.394991 seconds (23.63 M allocations: 1.180 GiB, 32.24% gc time)

MetaPhylo.Tree with 54327 leaves.

    Rooted: false

    Rerootable: true

julia> freeze(big_tree)

MetaPhylo.StaticTree with 54327 leaves.

    Rooted: false

    branch_data: NamedTuple{(:length,), Tuple{Float64}}

    node_data: NamedTuple{(), Tuple{}}

```