Metadata-Version: 2.4
Name: tact
Version: 1.0.1
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: >=3.12
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
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Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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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 tool for stochastic polytomy resolution, and generates complete phylogenies from incomplete ones. It uses birth-death-sampling estimators across an ultrametric phylogeny to generate branching times for unsampled taxa, using taxonomic information to compatibly place these unsampled taxa onto a backbone phylogeny.

## Getting started with TACT

* [Install TACT](https://tact.jonathanchang.org/install/)
* [Read the background](https://tact.jonathanchang.org/background/)
* [Try the tutorial](https://tact.jonathanchang.org/tutorial/)
* [Check the commands](https://tact.jonathanchang.org/commands/)
* [Solutions to common problems](https://tact.jonathanchang.org/troubleshooting/)

## Citation

If you use TACT in your research, 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 builds on foundational work in stochastic polytomy resolution, particularly:

* 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).

