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Open Source Science

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

Science Score: 20.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.6%) to scientific vocabulary

Keywords

biodiversity bioinformatics julia phylogeny
Last synced: 11 months ago · JSON representation

Repository

Phylogenetic trees with metadata by Julia based on Graphs.jl and AbstractTrees.jl.

Basic Info
  • Host: GitHub
  • Owner: banhbio
  • License: mit
  • Language: Julia
  • Default Branch: main
  • Homepage:
  • Size: 240 KB
Statistics
  • Stars: 4
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
biodiversity bioinformatics julia phylogeny
Created over 3 years ago · Last pushed over 3 years ago
Metadata Files
Readme License

README.md

MetaPhylo

Stable Dev Build Status Coverage DOI

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 and implemented with Graphs.jl and 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 bigtree = Newick.File("/path/to/bigtree") |> 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(bigtree) MetaPhylo.StaticTree with 54327 leaves. Rooted: false branchdata: NamedTuple{(:length,), Tuple{Float64}} node_data: NamedTuple{(), Tuple{}} ```

Owner

  • Name: Hiroki Ban
  • Login: banhbio
  • Kind: user
  • Location: Kyoto, Japan

GitHub Events

Total
Last Year

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 107
  • Total Committers: 2
  • Avg Commits per committer: 53.5
  • Development Distribution Score (DDS): 0.065
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
banhbio b****n@k****p 100
CompatHelper Julia c****y@j****g 7
Committer Domains (Top 20 + Academic)
julialang.org: 1 kuicr.kyoto-u.ac.jp: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 1
  • Total pull requests: 21
  • Average time to close issues: less than a minute
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.67
  • Merged pull requests: 21
  • Bot issues: 0
  • Bot pull requests: 7
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • JuliaTagBot (1)
Pull Request Authors
  • banhbio (14)
  • github-actions[bot] (7)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
juliahub.com: MetaPhylo

Phylogenetic trees with metadata by Julia based on Graphs.jl and AbstractTrees.jl.

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 9.9%
Average: 36.2%
Dependent packages count: 38.9%
Stargazers count: 42.3%
Forks count: 53.5%
Last synced: 12 months ago

Dependencies

.github/workflows/CI.yml actions
  • actions/checkout v2 composite
  • codecov/codecov-action v2 composite
  • julia-actions/cache v1 composite
  • julia-actions/julia-buildpkg v1 composite
  • julia-actions/julia-docdeploy v1 composite
  • julia-actions/julia-processcoverage v1 composite
  • julia-actions/julia-runtest v1 composite
  • julia-actions/setup-julia v1 composite
.github/workflows/TagBot.yml actions
  • JuliaRegistries/TagBot v1 composite