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tact

Taxonomy addition for complete trees

https://github.com/jonchang/tact

Science Score: 57.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.6%) to scientific vocabulary

Keywords

python

Keywords from Contributors

cryptocurrencies graph-generation mesh energy-systems simulator networking pairings polynomials distributed interactive
Last synced: 6 months ago · JSON representation ·

Repository

Taxonomy addition for complete trees

Basic Info
Statistics
  • Stars: 4
  • Watchers: 2
  • Forks: 2
  • Open Issues: 2
  • Releases: 22
Topics
python
Created over 8 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

TACT: Taxonomic Addition for Complete Trees

PyPI Build status Docker Hub

TACT is a Python app for stochastic polytomy resolution. It uses birth-death-sampling estimators across an ultrametric phylogeny to generate branching times for unsampled taxa, using taxonomic information to compatibly place new taxa onto a backbone phylogeny.

Getting started with TACT

Citation

TACT is described more fully in its manuscript. If you use TACT, please cite:

  • Chang, J., Rabosky, D. L., & Alfaro, M. E. (2019). Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions. Systematic Biology. doi:10.1093/sysbio/syz081

TACT owes its existence to much foundational work in the area of stochastic polytomy resolution, namely PASTIS and CorSiM.

  • Thomas, G. H., Hartmann, K., Jetz, W., Joy, J. B., Mimoto, A., & Mooers, A. O. (2013). PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences. Methods in Ecology and Evolution, 4(11), 1011–1017. doi:10.1111/2041-210x.12117

  • Cusimano, N., Stadler, T., & Renner, S. S. (2012). A New Method for Handling Missing Species in Diversification Analysis Applicable to Randomly or Nonrandomly Sampled Phylogenies. Systematic Biology, 61(5), 785–792. doi:10.1093/sysbio/sys031

Sponsorship

Please consider sponsoring the ongoing maintenance of TACT via GitHub Sponsors.

Initial development was supported by a National Science Foundation Doctoral Dissertation Improvement Grant (DEB-1601830).

Owner

  • Name: Jonathan Chang
  • Login: jonchang
  • Kind: user
  • Location: Los Angeles

Citation (CITATION.cff) 

cff-version: 1.2.0
repository-code: "https://github.com/jonchang/tact"
url: "https://tact.jonathanchang.org/"
title: "TACT: Taxonomic Addition for Complete Trees"
authors:
- family-names: "Chang"
  given-names: "Jonathan"
  orcid: "https://orcid.org/0000-0002-3811-1254"
  email: "me@jonathanchang.org"
message: "Please cite:"
preferred-citation:
  type: article
  authors:
  - family-names: "Chang"
    given-names: "Jonathan"
    orcid: "https://orcid.org/0000-0002-3811-1254"
    email: "me@jonathanchang.org"
  - family-names: "Rabosky"
    given-names: "Daniel L"
  - family-names: "Alfaro"
    given-names: "Michael E"
  doi: "10.1093/sysbio/syz081"
  journal: "Systematic Biology"
  month: 5
  start: 602
  end: 611
  title: "Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions"
  issue: 3
  volume: 69
  year: 2020

GitHub Events

Total
  • Watch event: 1
  • Delete event: 11
  • Issue comment event: 5
  • Push event: 7
  • Pull request event: 12
  • Create event: 8
Last Year
  • Watch event: 1
  • Delete event: 11
  • Issue comment event: 5
  • Push event: 7
  • Pull request event: 12
  • Create event: 8

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 613
  • Total Committers: 4
  • Avg Commits per committer: 153.25
  • Development Distribution Score (DDS): 0.491
Past Year
  • Commits: 14
  • Committers: 2
  • Avg Commits per committer: 7.0
  • Development Distribution Score (DDS): 0.429
Top Committers
Name Email Commits
Jonathan Chang j****1@g****m 312
dependabot[bot] 4****] 177
dependabot-preview[bot] 2****] 123
Joseph W. Brown p****b@g****m 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 5
  • Total pull requests: 146
  • Average time to close issues: 7 days
  • Average time to close pull requests: 15 days
  • Total issue authors: 4
  • Total pull request authors: 2
  • Average comments per issue: 3.8
  • Average comments per pull request: 0.32
  • Merged pull requests: 117
  • Bot issues: 0
  • Bot pull requests: 124
Past Year
  • Issues: 0
  • Pull requests: 24
  • Average time to close issues: N/A
  • Average time to close pull requests: 13 days
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.46
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 17
View more stats
Top Authors
Issue Authors
  • jonchang (2)
  • pbfrandsen (1)
  • jsoghigian (1)
  • dependabot[bot] (1)
  • Cactusolo (1)
Pull Request Authors
  • dependabot[bot] (134)
  • jonchang (22)
Top Labels
Issue Labels
bug (1) dependencies (1) github_actions (1)
Pull Request Labels
dependencies (134) python (70) github_actions (60) docker (4)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 60 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 18
  • Total maintainers: 1
pypi.org: tact

Taxonomic addition for complete trees: Adds tips to a backbone phylogeny using taxonomy simulated with birth-death models

  • Versions: 18
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 60 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 19.1%
Dependent repos count: 21.6%
Average: 24.3%
Stargazers count: 25.0%
Downloads: 45.7%
Maintainers (1)
jonchang
Last synced: 6 months ago

Dependencies

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  • click 8.1.3
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  • python >= 3.8, < 3.11
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  • toml ^0.10
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Dockerfile docker
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