tact 0.8.0

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 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
• Read the background
• Try the tutorial
• Check the commands
• Solutions to common problems

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:

• 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

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).