treetools

Create, modify and analyse phylogenetic trees in R

Science Score: 59.0%

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

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
1 of 5 committers (20.0%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (12.3%) to scientific vocabulary

Keywords

cran evolutionary-biology phylogenetic-trees phylogenetics r-package

Keywords from Contributors

graphics consensus-tree plotting-in-r ternary-plots bioinformatics morphological-analysis research-tool tree-search comparison quartet

Last synced: 6 months ago · JSON representation

Repository

Create, modify and analyse phylogenetic trees in R

Basic Info

Host: GitHub
Owner: ms609
Language: R
Default Branch: main
Homepage: https://ms609.github.io/TreeTools/
Size: 22.6 MB

Statistics

Stars: 23
Watchers: 3
Forks: 7
Open Issues: 19
Releases: 35

Topics

cran evolutionary-biology phylogenetic-trees phylogenetics r-package

Created over 6 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing Code of conduct Codemeta

TreeTools

'TreeTools' is an R package that provides efficient implementations of functions for the creation, modification and analysis of phylogenetic trees.

Applications include: generation of trees with specified shapes; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of node support; calculation of ancestor-descendant relationships; import and export of trees from Newick, Nexus and TNT formats; and analysis of partitions and cladistic information.

It complements packages such as 'ape', 'phangorn' and 'phytools', aiming for efficient and robust implementations of functions, typically applied to unweighted trees (i.e. those without edge lengths).

Installation

Install and load the library from CRAN as follows: r install.packages("TreeTools") library("TreeTools")

Install the very latest version, which may be under development, with: r if (!require("devtools")) install.packages("devtools") devtools::install_github("ms609/TreeTools")

Please note that the 'TreeTools' project is released with a Contributor Code of Conduct. By contributing to this project, you agree to its terms.

Owner

Name: Martin R. Smith
Login: ms609
Kind: user
Location: Durham, UK
Company: Department of Earth Sciences, Durham University

Website: https://orcid.org/0000-0001-5660-1727
Twitter: PalaeoSmith
Repositories: 21
Profile: https://github.com/ms609

Palaeontology & phylogenetics

CodeMeta (codemeta.json)

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "identifier": "TreeTools",
  "description": "Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.",
  "name": "TreeTools: Create, Modify and Analyse Phylogenetic Trees",
  "relatedLink": "https://ms609.github.io/TreeTools/",
  "codeRepository": "https://github.com/ms609/TreeTools/",
  "issueTracker": "https://github.com/ms609/TreeTools/issues/",
  "license": "https://spdx.org/licenses/GPL-3.0",
  "version": "2.0.0",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 4.5.2 (2025-10-31)",
  "provider": {
    "@id": "https://cran.r-project.org",
    "@type": "Organization",
    "name": "Comprehensive R Archive Network (CRAN)",
    "url": "https://cran.r-project.org"
  },
  "author": [
    {
      "@type": "Person",
      "givenName": "Martin R.",
      "familyName": "Smith",
      "email": "martin.smith@durham.ac.uk",
      "@id": "https://orcid.org/0000-0001-5660-1727"
    }
  ],
  "copyrightHolder": [
    {
      "@type": "Person",
      "givenName": "Martin R.",
      "familyName": "Smith",
      "email": "martin.smith@durham.ac.uk",
      "@id": "https://orcid.org/0000-0001-5660-1727"
    },
    {
      "@type": "Person",
      "givenName": "Emmanuel",
      "familyName": "Paradis",
      "@id": "https://orcid.org/0000-0003-3092-2199"
    },
    {
      "@type": "Person",
      "givenName": "Robert",
      "familyName": "Noble",
      "@id": "https://orcid.org/0000-0002-8057-4252"
    }
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Martin R.",
      "familyName": "Smith",
      "email": "martin.smith@durham.ac.uk",
      "@id": "https://orcid.org/0000-0001-5660-1727"
    }
  ],
  "softwareSuggestions": [
    {
      "@type": "SoftwareApplication",
      "identifier": "spelling",
      "name": "spelling",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=spelling"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "knitr",
      "name": "knitr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=knitr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "phangorn",
      "name": "phangorn",
      "version": ">= 2.2.1",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=phangorn"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "Rcpp",
      "name": "Rcpp",
      "version": ">= 1.0.8",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=Rcpp"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rmarkdown",
      "name": "rmarkdown",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "testthat",
      "name": "testthat",
      "version": ">= 3.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testthat"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "TreeDist",
      "name": "TreeDist",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=TreeDist"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "TreeSearch",
      "name": "TreeSearch",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=TreeSearch"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "vdiffr",
      "name": "vdiffr",
      "version": ">= 1.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=vdiffr"
    }
  ],
  "softwareRequirements": {
    "1": {
      "@type": "SoftwareApplication",
      "identifier": "R",
      "name": "R",
      "version": ">= 3.6.0"
    },
    "2": {
      "@type": "SoftwareApplication",
      "identifier": "ape",
      "name": "ape",
      "version": ">= 5.6",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=ape"
    },
    "3": {
      "@type": "SoftwareApplication",
      "identifier": "bit64",
      "name": "bit64",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=bit64"
    },
    "4": {
      "@type": "SoftwareApplication",
      "identifier": "fastmatch",
      "name": "fastmatch",
      "version": ">= 1.1.3",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=fastmatch"
    },
    "5": {
      "@type": "SoftwareApplication",
      "identifier": "methods",
      "name": "methods"
    },
    "6": {
      "@type": "SoftwareApplication",
      "identifier": "PlotTools",
      "name": "PlotTools",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=PlotTools"
    },
    "7": {
      "@type": "SoftwareApplication",
      "identifier": "RCurl",
      "name": "RCurl",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=RCurl"
    },
    "8": {
      "@type": "SoftwareApplication",
      "identifier": "Rdpack",
      "name": "Rdpack",
      "version": ">= 2.3",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=Rdpack"
    },
    "9": {
      "@type": "SoftwareApplication",
      "identifier": "stringi",
      "name": "stringi",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=stringi"
    },
    "SystemRequirements": "C++17"
  },
  "fileSize": "1763.04KB",
  "citation": [
    {
      "@type": "SoftwareSourceCode",
      "datePublished": "2019",
      "author": [
        {
          "@type": "Person",
          "givenName": [
            "Martin",
            "R."
          ],
          "familyName": "Smith",
          "email": "martin.smith@durham.ac.uk"
        }
      ],
      "name": "TreeTools: create, modify and analyse phylogenetic trees",
      "identifier": "10.32614/CRAN.package.TreeTools",
      "description": "R package version 2.0.0",
      "@id": "https://doi.org/10.32614/CRAN.package.TreeTools",
      "sameAs": "https://doi.org/10.32614/CRAN.package.TreeTools"
    }
  ]
}

GitHub Events

Total

Create event: 40
Release event: 5
Issues event: 11
Watch event: 5
Delete event: 23
Issue comment event: 168
Push event: 383
Pull request review comment event: 28
Pull request review event: 21
Pull request event: 63

Last Year

Create event: 40
Release event: 5
Issues event: 11
Watch event: 5
Delete event: 23
Issue comment event: 168
Push event: 383
Pull request review comment event: 28
Pull request review event: 21
Pull request event: 63

Committers

Last synced: about 1 year ago

All Time

Total Commits: 1,112
Total Committers: 5
Avg Commits per committer: 222.4
Development Distribution Score (DDS): 0.491

Past Year

Commits: 136
Committers: 2
Avg Commits per committer: 68.0
Development Distribution Score (DDS): 0.132

Top Committers

Name	Email	Commits
Martin Smith	m**s@g**m	566
Martin R. Smith	1****9	438
Martin R. Smith	p**8@d**k	58
GitHub Actions	a**s@g**m	49
Hadley Wickham	h**m@g**m	1

Committer Domains (Top 20 + Academic)

github.com: 1 durham.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 55
Total pull requests: 137
Average time to close issues: 8 months
Average time to close pull requests: about 2 months
Total issue authors: 13
Total pull request authors: 3
Average comments per issue: 1.11
Average comments per pull request: 1.07
Merged pull requests: 105
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 6
Pull requests: 46
Average time to close issues: 10 days
Average time to close pull requests: about 10 hours
Issue authors: 4
Pull request authors: 2
Average comments per issue: 2.17
Average comments per pull request: 1.5
Merged pull requests: 26
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

ms609 (40)
marwa38 (2)
theo-allnutt-bioinformatics (2)
stitam (2)
kuang-da (1)
jc17659 (1)
jblandis (1)
osourcenewbie (1)
saramortara (1)
RussellGarwood (1)
HS6986 (1)
noranekonobokkusu (1)
EJchemoiwa (1)

Pull Request Authors

ms609 (133)
Copilot (3)
hadley (1)

Top Labels

Issue Labels

help wanted (1)

Pull Request Labels

Dependencies

DESCRIPTION cran

R >= 3.4.0 depends
ape >= 5.6 depends
R.cache * imports
Rdpack >= 2.3 imports
bit64 * imports
colorspace * imports
fastmatch >= 1.1.3 imports
lifecycle * imports
methods * imports
Rcpp >= 1.0.8 suggests
knitr * suggests
phangorn >= 2.2.1 suggests
rmarkdown * suggests
spelling * suggests
testthat >= 3.0 suggests
vdiffr >= 1.0.0 suggests

.github/workflows/ASan.yml actions

actions/cache v3 composite
actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

.github/workflows/R-CMD-check.yml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/RcppDeepState.yml actions

FabrizioSandri/RcppDeepState-action main composite
actions/checkout v3 composite

.github/workflows/codemeta.yml actions

ms609/actions/codemeta main composite

.github/workflows/memcheck.yml actions

actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yml actions

ms609/actions/pkgdown main composite

.github/workflows/rchk.yml actions

actions/checkout v3 composite
r-lib/actions/run-rchk v2 composite
randy3k/gh-actions/r-install-deps main composite

.github/workflows/revdepcheck.yml actions

ms609/actions/revdepcheck main composite

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

treetools

Science Score: 59.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

TreeTools

Installation

Owner

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies