TACT: Taxonomic Addition for Complete Trees
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
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
TACT builds on foundational work in stochastic polytomy resolution, particularly:
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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
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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).
1 maintainer
Metadata
1 maintainer
Release files for tact 0.8.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
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| tact-0.8.0.tar.gz | 43.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| tact-0.8.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 72.4 kB
Release files / tact-0.8.0.tar.gz
| Download URL | tact-0.8.0.tar.gz |
|---|---|
| Size | 43.7 kB |
| Tags | Source |
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| Size | 28.7 kB |
| Tags | Python 3 |
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