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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

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.

Homebrew

Using Homebrew is the recommended way to install TACT. Install Homebrew on macOS or Install Homebrew on Linux or Windows 10. Once Homebrew has been installed, run

brew install jonchang/biology/tact

pipx

If you are unable or unwilling to use Homebrew, the next recommended way to install TACT is via pipx. Install pipx, then run:

pipx install tact

If you have PyPy3 installed (via e.g. brew install pypy3 or some other source) and feel particularly adventurous, you can try to install a faster PyPy version using:

pipx install --python pypy3 tact

Note that this will take much longer to install, and the installation will almost certainly fail unless you have the proper compilers set up. If it succeeds though, you should see a rather dramatic improvement in TACT's performance.

Docker

You can also try using the Docker image if you can't get your Python to cooperate. 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/master/examples/Carangaria.csv
curl -LO https://raw.githubusercontent.com/jonchang/tact/master/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

One benefit of using the Docker image is that it automatically uses PyPy3, which can speed up your TACT run, but might also be slower on macOS. Here's a screencast of what this looks like:

asciicast

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/master/examples/Carangaria.csv
curl -LO https://raw.githubusercontent.com/jonchang/tact/master/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
$ git push

A GitHub Actions workflow will build and publish the new version on PyPI.

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.

Project details


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