Physcraper 1.0.0

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# Welcome to Physcraper’s repository!

[](https://travis-ci.org/McTavishLab/physcraper)[](https://physcraper.readthedocs.io/en/main/)[](https://codecov.io/gh/McTavishLab/physcraper)

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## Automated gene tree updating <br> with the Open Tree of Life

Use a phylogenetic tree and a DNA alignment to automatically find and add nucleotide sequences from a genetic database, to reproducibly improve and advance phylogenetic knowledge within a biological group.

Physcraper relies on [taxonomic](https://tree.opentreeoflife.org/about/taxonomy-version/ott3.3) and [phylogenetic](https://github.com/OpenTreeOfLife/phylesystem-1) resources and [programmatic tools](https://github.com/OpenTreeOfLife/germinator/wiki/Open-Tree-of-Life-Web-APIs) from the [Open Tree of Life](https://tree.opentreeoflife.org/opentree/argus/opentree12.3@ott93302) project.

Physcraper also leverages on programmatic tools from the [TreeBASE](https://treebase.org/treebase-web/urlAPI.html) project and [NCBI](https://www.ncbi.nlm.nih.gov/home/develop/api/), as well as multiple software projects listed as [requirements](#requirements) below, to create an automatic and reproducible workflow for phylogenetics.

You are now on the code repository. Please refer to Physcraper’s [documentation website](https://physcraper.readthedocs.io/en/main/) for more details on:

• [installation](https://physcraper.readthedocs.io/en/main/install.html) instructions using an Anaconda or a Virtualenv Python virtual environment,

• [function](https://physcraper.readthedocs.io/en/main/apidocs.html) usage,

• finding and choosing a [starting dataset](https://physcraper.readthedocs.io/en/main/find-trees.html),

• [running](https://physcraper.readthedocs.io/en/main/run.html) a full analysis,

• [visualizing and analysing](https://physcraper.readthedocs.io/en/main/results.html) results,

• real life [examples](https://physcraper.readthedocs.io/en/main/examples.html), and

• tools for [developers](https://physcraper.readthedocs.io/en/main/CONTRIBUTING.html).

hamster:

palm_tree:

frog:

ear_of_rice:

panda_face:

tulip:

octopus:

blossom:

whale:

mushroom:

ant:

cactus:

fish:

maple_leaf:

water_buffalo:

🦠 :shell: :bug: :octocat:

## Citation

If you use Physcraper, please cite:

• Sánchez-Reyes, L.L., M. Kandziora, & E.J McTavish. (2021). Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life. BMC Bioinformatics 22, 355. doi: [doi.org/10.1186/s12859-021-04274-6](https://doi.org/10.1186/s12859-021-04274-6). <br><br>

• Open Tree of Life, B. Redelings, L.L. Sanchez Reyes, K.A. Cranston, J. Allman, M.T. Holder, & E.J. McTavish. (2019). Open Tree of Life Synthetic Tree (Version 12.3). Zenodo. doi: [10.5281/zenodo.3937741](https://doi.org/10.5281/zenodo.3937741)

## License

Physcraper is made available through the [GNU General Public License v3.0](https://github.com/McTavishLab/physcraper/blob/main/LICENSE)

## Contact

The tool is under active development in the [McTavish Lab](https://mctavishlab.github.io/). Please post a GitHub issue [here](https://github.com/McTavishLab/physcraper/issues) or contact <ejmctavish@ucmerced.edu> if you need any help or have feedback.

## Requirements

Physcraper requires the user to install:

• [Anaconda](https://docs.anaconda.com/anaconda/install/) <br> Anaconda Software Distribution. Computer software. Vers. 4.8.0. Anaconda, July. 2021. Web. <https://anaconda.com>

• [Virtualenv](https://pypi.org/project/virtualenv/)

• [MUSCLE](https://www.ebi.ac.uk/Tools/msa/muscle/) <br> Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004 Mar 19;32(5):1792-7. doi: [10.1093/nar/gkh340](https://doi.org/10.1093/nar/gkh340)

• [RAxML](https://cme.h-its.org/exelixis/web/software/raxml/) <br> Stamatakis, Alexandros. “RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.” Bioinformatics 30.9 (2014): 1312-1313. doi: [10.1093/bioinformatics/btu033](https://doi.org/10.1093/bioinformatics/btu033)

• [BLAST +](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) <br> This software is only needed if using a local genetic database. Note that BLAST + is automatically installed when [installing Physcraper using Anaconda](https://physcraper.readthedocs.io/en/stable/install.html#anaconda-virtual-environment). <br> Camacho, C., Coulouris, G., Avagyan, V. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009). doi: [10.1186/1471-2105-10-421](https://doi.org/10.1186/1471-2105-10-421)

<br> Physcraper relies on the following Python packages that are <b>automatically</b> installed:

• [argparse](https://docs.python.org/3/library/argparse.html)

• [biopython](https://biopython.org/) <br> Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422–1423.

• [configparser](https://docs.python.org/3/library/configparser.html)

• [coverage](https://coverage.readthedocs.io/)

• [DateTime](https://docs.python.org/3/library/datetime.html)

• [DendroPy](https://dendropy.org/primer/index.html) <br> Sukumaran, J and MT Holder. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26: 1569-1571 doi: [10.1093/bioinformatics/btq228](https://doi.org/10.1093/bioinformatics/btq228)

• [future](https://python-future.org/)

• [m2r2](https://pypi.org/project/m2r2/)

• [nexson](https://github.com/OpenTreeOfLife/nexson)

• [numpy](https://numpy.org/) <br> Harris, C. R., Millman, K. J., van der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., … Oliphant, T. E. (2020). Array programming with NumPy. Nature, 585, 357–362. doi: [10.1038/s41586-020-2649-2](https://doi.org/10.1038/s41586-020-2649-2)

• [OpenTree](https://github.com/OpenTreeOfLife/python-opentree) <br> Emily Jane McTavish, Luna Luisa Sanchez-Reyes, Mark T. Holder. (2020). OpenTree: A Python package for Accessing and Analyzing data from the Open Tree of Life. BioRxiv 2020.12.14.422759 doi: [10.1101/2020.12.14.422759](https://doi.org/10.1101/2020.12.14.422759)

• [pandas](https://pandas.pydata.org/) <br> McKinney, W., & others. (2010). Data structures for statistical computing in python. In Proceedings of the 9th Python in Science Conference (Vol. 445, pp. 51–56).

• [pytest](https://pytest.org/)

• [pytest-cov](https://pytest-cov.readthedocs.io/)

• [pytest-xdist](https://pypi.org/project/pytest-xdist/)

• [recommonmark](https://recommonmark.readthedocs.io/)

• [requests](https://docs.python-requests.org/) <br> Chandra, R. V., & Varanasi, B. S. (2015). Python requests essentials. Packt Publishing Ltd.

• [sh](https://amoffat.github.io/sh/)

• [sphinx](https://www.sphinx-doc.org/)

• [urllib3](https://urllib3.readthedocs.io/)