Taxonomic addition for complete trees: Adds tips to a backbone phylogeny using taxonomy simulated with birth-death models
TACT: Taxonomic Addition for Complete Trees
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
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
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).
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