https://github.com/jonchang/tact

Taxonomy addition for complete trees
https://github.com/jonchang/tact

python

Last synced: about 1 month ago
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Taxonomy addition for complete trees

• Host: GitHub
• URL: https://github.com/jonchang/tact
• Owner: jonchang
• License: mit
• Created: 2017-11-22T01:38:24.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2025-03-08T21:11:41.000Z (3 months ago)
• Last Synced: 2025-05-05T05:06:43.922Z (about 1 month ago)
• Topics: python
• Language: Python
• Homepage: https://tact.jonathanchang.org
• Size: 761 KB
• Stars: 4
• Watchers: 2
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Citation: CITATION.cff

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README

        
# TACT: Taxonomic Addition for Complete Trees

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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

* [Installing](https://tact.jonathanchang.org/install/)

* [Introduction and background](https://tact.jonathanchang.org/background/)

* [Example analysis](https://tact.jonathanchang.org/tutorial/)

* [Troubleshooting problems](https://tact.jonathanchang.org/troubleshooting/)

## 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](https://doi.org/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](https://doi.org/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](https://doi.org/10.1093/sysbio/sys031)

## Sponsorship

Please consider sponsoring the ongoing maintenance of TACT via [GitHub Sponsors](https://github.com/sponsors/jonchang).

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