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Taxonomic addition for complete trees: Adds tips to a backbone phylogeny using taxonomy simulated with birth-death models

Project description

TACT - Taxonomy addition for complete trees

PyPI Build status Docker Hub

Adds tips to a backbone phylogeny using taxonomy simulated with birth-death models

Installation

TACT requires Python 3. When possible, we recommend using the PyPy 3 implementation as it can significantly speed up TACT analyses, particularly on large datasets. In addition, TACT depends on the click, DendroPy, NumPy, and SciPy packages.

Docker

If you can use Docker, this is the recommended method as it is both convenient to install and fast for large datasets thanks to PyPy.

Install Docker Desktop and run the following to download the TACT image:

docker pull jonchang/tact:latest

Then, run TACT from the container image, giving it access to your current working directory:

mkdir -p examples
cd examples
curl -LO https://raw.githubusercontent.com/jonchang/tact/HEAD/examples/Carangaria.csv
curl -LO https://raw.githubusercontent.com/jonchang/tact/HEAD/examples/Carangaria.tre
docker run -it -v "$(pwd)":/workdir -w /workdir jonchang/tact tact_build_taxonomic_tree Carangaria.csv --output Carangaria.taxonomy.tre
docker run -it -v "$(pwd)":/workdir -w /workdir jonchang/tact tact_add_taxa --backbone Carangaria.tre --taxonomy Carangaria.taxonomy.tre --output Carangaria.tacted

Here's a screencast of using the Docker commands:

asciicast

Homebrew

Install Homebrew on macOS or Install Homebrew on Linux or Windows 10. Once Homebrew has been installed, run

brew install jonchang/biology/tact

This is easy to install if you don't have Docker access, but for large datasets, this can be as much as 5x slower.

pipx

Install pipx, then run:

pipx install tact

If you have PyPy3 installed, you can try to install a faster version using:

pipx install --python pypy3 tact

Note that this will take much longer to install and could fail if the proper dependencies (mainly openblas) aren't set up. On macOS, you'll need to run brew install openblas gcc pypy3 pipx, force-link openblas, and set the MACOSX_DEPLOYMENT_TARGET environment variable to your macOS version (e.g., 11.0).

Other

Other ways of installing TACT, including unpacking the tarball somewhere or directly using pip, are neither supported nor recommended.

Example

Files used are in the examples folder.

curl -LO https://raw.githubusercontent.com/jonchang/tact/HEAD/examples/Carangaria.csv
curl -LO https://raw.githubusercontent.com/jonchang/tact/HEAD/examples/Carangaria.tre

Build a taxonomic tree using the provided CSV file. Run tact_build_taxonomic_tree --help to see the required format for this file.

$ tact_build_taxonomic_tree Carangaria.csv --output Carangaria.taxonomy.tre
Output written to: Carangaria.taxonomy.tre

Carangaria.taxonomy.tre now contains a Newick phylogeny with many polytomies and named nodes indicating relevant taxonomic ranks. Now run the TACT stochastic polytomy resolver algorithm in conjunction with the backbone phylogeny Caragaria.tre.

$ tact_add_taxa --backbone Carangaria.tre --taxonomy Carangaria.taxonomy.tre --output Carangaria.tacted --verbose --verbose
Rates  [####################################]  226/226
TACT  [####################################]  642/642  Carangaria

There will be several files created with the prefix Carangaria.tacted. These include newick.tre and nexus.tre (your primary output in the form of Newick and NEXUS format phylogenies), rates.csv (estimated diversification rates on the backbone phylogeny), and log.txt (extremely verbose output on what TACT is doing and why).

You should check the TACT results now for any issues:

$ tact_check_results Carangaria.tacted.newick.tre --backbone Carangaria.tre --taxonomy Carangaria.taxonomy.tre > checkresults.csv

Open up checkresults.csv in your favorite spreadsheet viewer and check the warnings column for any issues.

Contributing

Development on TACT uses poetry. Simply clone the repository and install:

$ git clone https://github.com/jonchang/tact.git
$ cd tact
$ poetry install

When releasing a new version of tact, run its tests and bump its revision like so:

$ poetry run pytest  # optionally with --script-launch-mode=subprocess
$ poetry version patch  # or minor, etc.
$ git commit -p
$ git tag VERSION  # (0.4.0)
$ git push --atomic origin BRANCH_NAME TAG  # (master, v0.4.0)

A GitHub Actions workflow will build and publish the new version on PyPI, as well as releasing container images to Docker Hub and GitHub Packages.

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

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

Sponsorship

Please consider sponsoring the maintenance of TACT via GitHub Sponsors.

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