Metadata-Version: 2.4
Name: tact
Version: 0.7.0
Summary: Taxonomic addition for complete trees: Adds tips to a backbone phylogeny using taxonomy simulated with birth-death models
License-Expression: MIT
License-File: LICENSE
Author: Jonathan Chang
Author-email: me@jonathanchang.org
Maintainer: Jonathan Chang
Maintainer-email: me@jonathanchang.org
Requires-Python: >=3.10,<4
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Provides-Extra: dev
Requires-Dist: DendroPy (>=4.5,<6.0)
Requires-Dist: click (>=8.3.1,<9.0.0)
Requires-Dist: hypothesis (>=6.148.0,<7.0.0) ; extra == "dev"
Requires-Dist: numpy (>=2.2,<3)
Requires-Dist: portion (>=2.2)
Requires-Dist: pytest (>=9.0.1,<10.0.0) ; extra == "dev"
Requires-Dist: pytest-benchmark (>=5.2.3,<6.0.0) ; extra == "dev"
Requires-Dist: pytest-console-scripts (>=1.4.1,<2.0.0) ; extra == "dev"
Requires-Dist: pytest-cov (>=7.0.0,<8.0.0) ; extra == "dev"
Requires-Dist: toml (>=0.10)
Project-URL: Documentation, https://tact.jonathanchang.org
Project-URL: Homepage, https://tact.jonathanchang.org
Project-URL: Repository, https://github.com/jonchang/tact
Project-URL: changelog, https://tact.jonathanchang.org/news/
Project-URL: issue, https://github.com/jonchang/tact/issues
Project-URL: sponsor, https://github.com/sponsors/jonchang
Description-Content-Type: text/markdown

# TACT: Taxonomic Addition for Complete Trees

[![PyPI](https://img.shields.io/pypi/v/tact.svg)](https://pypi.org/project/tact/)
[![Build status](https://github.com/jonchang/tact/workflows/Python%20package/badge.svg)](https://github.com/jonchang/tact/actions)
[![Docker Hub](https://img.shields.io/docker/pulls/jonchang/tact.svg)](https://hub.docker.com/r/jonchang/tact)

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).

