DendroPy 5
DendroPy 5: a mature Python library for phylogenetic computing - Published in JOSS (2024)
Science Score: 100.0%
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✓CITATION.cff file
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✓DOI references
Found 10 DOI reference(s) in README and JOSS metadata -
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7 of 35 committers (20.0%) from academic institutions -
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords from Contributors
Scientific Fields
Repository
A Python library for phylogenetic scripting, simulation, data processing and manipulation.
Basic Info
- Host: GitHub
- Owner: jeetsukumaran
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://pypi.org/project/DendroPy/.
- Size: 56.4 MB
Statistics
- Stars: 221
- Watchers: 14
- Forks: 58
- Open Issues: 20
- Releases: 0
Metadata Files
README.md
DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful phylogenetic operations, such as data conversion and tree posterior distribution summarization, are also distributed and installed as part of the libary. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipelines, or as a scripting "glue" that assembles and drives such pipelines.
The primary home page for DendroPy, with detailed tutorials and documentation, is at:
https://jeetsukumaran.github.io/DendroPy/
DendroPy is also hosted in the official Python Packaging Index (PyPI):
http://pypi.org/project/DendroPy/
Requirements and Installation
The current version of DendroPy requires Python 3.
You can install DendroPy by running::
$ python -m pip install dendropy
For Conda users, DendroPy can be installed from the conda-forge channel:
$ conda install -c conda-forge dendropy
More information is available here:
https://jeetsukumaran.github.io/DendroPy/downloading.html
Documentation
Full documentation is available here:
https://jeetsukumaran.github.io/DendroPy/
This includes:
- A comprehensive "getting started" primer.
- API documentation.
- Descriptions of data formats supported for reading/writing.
- Guidance for reporting issues, submitting feature requests, and contributing to DendroPy.
and more.
Citing
If you use any portion of DendroPy v5 in your research, please cite it as:
Moreno, M. A., Holder, M. T., & Sukumaran, J. (2024). DendroPy 5: a mature Python library for phylogenetic computing. Journal of Open Source Software, 9(101), 6943, https://doi.org/10.21105/joss.06943
For BibTex users:
bibtex
@misc{dendropy5,
doi = {10.21105/joss.06943},
url = {https://doi.org/10.21105/joss.06943},
year = {2024},
publisher = {The Open Journal},
volume = {9},
number = {101},
pages = {6943},
author = {Matthew Andres Moreno and Mark T. Holder and Jeet Sukumaran},
title = {DendroPy 5: a mature Python library for phylogenetic computing},
journal = {Journal of Open Source Software}
}
`
Earlier DendroPy versions can be cited as:
Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26: 1569-1571. https://doi.org/10.1093/bioinformatics/btq228
Consider also leaving a star on GitHub!
License and Warranty
Please see the file "LICENSE.rst" for details.
Developers
```
Owner
- Name: Jeet Sukumaran
- Login: jeetsukumaran
- Kind: user
- Company: http://sukumaranlab.org
- Website: http://jeetblogs.org
- Repositories: 142
- Profile: https://github.com/jeetsukumaran
JOSS Publication
DendroPy 5: a mature Python library for phylogenetic computing
Authors
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America, Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI, United States of America, Michigan Institute for Data and AI in Society, University of Michigan, Ann Arbor, MI, United States of America
Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America, Biodiversity Institute, University of Kansas, Lawrence, KS, United States of America
Department of Biology, San Diego State University, San Diego, CA, United States of America
Editor
AHM Mahfuzur Rahman
Tags
phylogenetics phylogeny phylogenies phylogeography biology evolution evolutionary biology systematics coalescent population genetics phyloinformatics bioinformaticsCitation (CITATION.cff)
cff-version: "1.2.0"
authors:
- family-names: Moreno
given-names: Matthew Andres
orcid: "https://orcid.org/0000-0003-4726-4479"
- family-names: Holder
given-names: Mark T.
orcid: "https://orcid.org/0000-0001-5575-0536"
- family-names: Sukumaran
given-names: Jeet
orcid: "https://orcid.org/0000-0002-9222-9608"
doi: 10.5281/zenodo.13340136
message: If you use this software, please cite our article in the
Journal of Open Source Software.
preferred-citation:
authors:
- family-names: Moreno
given-names: Matthew Andres
orcid: "https://orcid.org/0000-0003-4726-4479"
- family-names: Holder
given-names: Mark T.
orcid: "https://orcid.org/0000-0001-5575-0536"
- family-names: Sukumaran
given-names: Jeet
orcid: "https://orcid.org/0000-0002-9222-9608"
date-published: 2024-09-23
doi: 10.21105/joss.06943
issn: 2475-9066
issue: 101
journal: Journal of Open Source Software
publisher:
name: Open Journals
start: 6943
title: "DendroPy 5: a mature Python library for phylogenetic
computing"
type: article
url: "https://joss.theoj.org/papers/10.21105/joss.06943"
volume: 9
title: "DendroPy 5: a mature Python library for phylogenetic computing"
GitHub Events
Total
- Issues event: 5
- Watch event: 12
- Delete event: 3
- Issue comment event: 20
- Push event: 44
- Pull request event: 11
- Fork event: 1
- Create event: 9
Last Year
- Issues event: 5
- Watch event: 12
- Delete event: 3
- Issue comment event: 20
- Push event: 44
- Pull request event: 11
- Fork event: 1
- Create event: 9
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jeet Sukumaran | j****n@g****m | 3,961 |
| Matthew Andres Moreno | m****g@g****m | 312 |
| Mark T. Holder | m****r@g****m | 283 |
| Connor Yang | c****5@g****m | 61 |
| Andrew Guy | a****y@b****u | 6 |
| dependabot[bot] | 4****] | 5 |
| David Pattinson | d****i@p****m | 5 |
| Nephrain | 9****n | 4 |
| April Wright | w****m@g****m | 3 |
| Steve Bond | b****y@g****m | 2 |
| allista | a****a@g****m | 2 |
| terrycojones | t****y@j****s | 2 |
| Derrick Zwickl | z****l@D****l | 1 |
| mholder | m****r@k****u | 1 |
| mgymrek | m****k@m****u | 1 |
| a g | a****i@b****) | 1 |
| Vachaspati | v****2@t****u | 1 |
| Pranjal Vachaspati | p****l@p****l | 1 |
| Mark Holder | m****r@j****) | 1 |
| Aleksei Morozov | a****2@e****m | 1 |
| Ben J Woodcroft | d****n@g****m | 1 |
| Chris Rosenthal | c****h@u****u | 1 |
| Emily Jane McTavish | e****h@g****m | 1 |
| wosnat | o****g@g****m | 1 |
| Harry Detering | h****g@g****m | 1 |
| Jamie R. Oaks | j****1@g****m | 1 |
| Jonathan Chang | j****1@g****m | 1 |
| Matthias Bussonnier | b****s@g****m | 1 |
| NicolaDM | n****5@g****m | 1 |
| Noah Amsel | e****5@g****m | 1 |
| and 5 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 85
- Total pull requests: 75
- Average time to close issues: about 2 years
- Average time to close pull requests: 8 months
- Total issue authors: 59
- Total pull request authors: 21
- Average comments per issue: 2.22
- Average comments per pull request: 1.09
- Merged pull requests: 51
- Bot issues: 0
- Bot pull requests: 15
Past Year
- Issues: 2
- Pull requests: 18
- Average time to close issues: 7 months
- Average time to close pull requests: 3 days
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 6.0
- Average comments per pull request: 1.0
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 9
Top Authors
Issue Authors
- mmore500 (13)
- psathyrella (3)
- mtholder (3)
- hyanwong (3)
- idavydov (2)
- nick-youngblut (2)
- niemasd (2)
- thekswenson (2)
- terrycojones (2)
- ericmjl (2)
- wrightaprilm (2)
- benjaminwilson (2)
- Wytamma (1)
- crosenth (1)
- dependabot[bot] (1)
Pull Request Authors
- mmore500 (55)
- dependabot[bot] (19)
- terrycojones (4)
- davipatti (2)
- evoling (2)
- SamStudio8 (1)
- balhoff (1)
- Carreau (1)
- Kuanhao-Chao (1)
- crosenth (1)
- joaks1 (1)
- actapia (1)
- NoahAmsel (1)
- pranjalv123 (1)
- jmenglund (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 21,664 last-month
- Total docker downloads: 475
- Total dependent packages: 33
- Total dependent repositories: 109
- Total versions: 30
- Total maintainers: 3
pypi.org: dendropy
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
- Homepage: http://github.com/jeetsukumaran/DendroPy
- Documentation: https://jeetsukumaran.github.io/DendroPy/
- License: BSD
-
Latest release: 5.0.8
published 7 months ago
Rankings
Maintainers (3)
Dependencies
- sphinxcontrib-napoleon *
- setuptools *