Physcraper
Project description
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# Welcome to Physcraper’s repository!
[![Build Status](https://travis-ci.org/McTavishLab/physcraper.svg?branch=main)](https://travis-ci.org/McTavishLab/physcraper)[![Documentation](https://readthedocs.org/projects/physcraper/badge/?version=main&style=flat)](https://physcraper.readthedocs.io/en/main/)[![codecov](https://codecov.io/gh/McTavishLab/physcraper/branch/main/graph/badge.svg)](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.
[sphinx](https://www.sphinx-doc.org/)
[urllib3](https://urllib3.readthedocs.io/)
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