Science Score: 33.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
○codemeta.json file
-
○.zenodo.json file
-
✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: plos.org -
✓Committers with academic emails
4 of 8 committers (50.0%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (15.1%) to scientific vocabulary
Keywords from Contributors
Repository
Python library to simulate evolutionary sequence data
Basic Info
Statistics
- Stars: 80
- Watchers: 8
- Forks: 24
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
Pyvolve
Pyvolve is an open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution. Please ensure you are using the most up-to-date version of Pyvolve! The current version is 1.1.0.
A detailed user manual for Pyvolve is available here, and API documentation for Pyvolve is available at https://sjspielman.github.io/pyvolve.
Pyvolve has several dependencies: * Biopython * Scipy and Numpy (with Numpy >= 1.7)
Currently, pyvolve development is occurring in Python3.x with absolutely no plans to return to Python2. The following examples therefore assume Python3 (which you may have on your computer named as python3 and not python!)
You can install Pyvolve directly using pip or easy_install (note that, if needed, these lines will install any missing dependencies for you!):
```bash
pip install pyvolve
OR
easy_install install pyvolve
``
Note that these commands might needsudo` in front, depending on your permissions.
To update your version of Pyvolve (for pip), simply use the --upgrade argument (again, possibly w/ sudo):
bash
pip install --upgrade pyvolve
Alternatively, you can download and install from source. Download the most recent version of Pyvolve from the Releases tab (https://github.com/sjspielman/pyvolve/releases), uncompress the file, and navigate into the pyvolve/ directory. From this directory, enter the following commands:
bash
sudo python setup.py install
sudo python setup.py test # optional, but recommended!
If you do not have root privileges, you can install Pyvolve for only you (the user!) with this line instead:
bash
python setup.py install --user
Please file any bugs and/or relay any questions under the Issues tab: https://github.com/sjspielman/pyvolve/issues.
If you use Pyvolve in your research, please cite the following:
Spielman, SJ and Wilke, CO. 2015. Pyvolve: A flexible Python module for simulating sequences along phylogenies. PLOS ONE. 10(9): e0139047.
@article{SpielmanWilke2015,
author = {Spielman, S. J. and Wilke, C. O.},
title = {Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies},
journal = {PLOS ONE},
year = {2015},
volume = 10,
pages = {e0139047}
}
Owner
- Name: Stephanie
- Login: sjspielman
- Kind: user
- Location: Philadelphia, PA
- Company: @AlexsLemonade
- Website: https://sjspielman.github.io
- Twitter: stephspiel
- Repositories: 74
- Profile: https://github.com/sjspielman
Computational biologist and data scientist
GitHub Events
Total
- Issues event: 1
- Fork event: 1
Last Year
- Issues event: 1
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Stephanie J Spielman | s****n@g****m | 587 |
| sjspielman | s****n@u****u | 183 |
| Stephanie J. Spielman | s****n@r****u | 29 |
| Stephanie Spielman | s****n@m****l | 10 |
| Stephanie Spielman | s****5@p****u | 2 |
| Claus Wilke | w****e@a****u | 1 |
| Karl Keat | k****t@g****m | 1 |
| jbloom | j****m@f****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 21
- Total pull requests: 4
- Average time to close issues: 21 days
- Average time to close pull requests: 4 days
- Total issue authors: 16
- Total pull request authors: 4
- Average comments per issue: 2.71
- Average comments per pull request: 1.25
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dschrempf (2)
- dlaehnemann (2)
- kfuku52 (2)
- niemasd (2)
- idavydov (2)
- ksw9 (1)
- rhr (1)
- yuanning-li (1)
- Becheler (1)
- y9c (1)
- EldhosePoulose (1)
- rLannes (1)
- markkessler66 (1)
- thekswenson (1)
- jbloom (1)
Pull Request Authors
- KarlKeat (1)
- idavydov (1)
- jbloom (1)
- tkchafin (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- pypi 462 last-month
-
Total dependent packages: 2
(may contain duplicates) -
Total dependent repositories: 11
(may contain duplicates) - Total versions: 36
- Total maintainers: 2
pypi.org: pyvolve
Sequence simulation along phylogenies according to continuous-time Markov models
- Homepage: https://github.com/sjspielman/pyvolve
- Documentation: https://pyvolve.readthedocs.io/
- License: other
-
Latest release: 1.1.0
published over 4 years ago
Rankings
Maintainers (1)
spack.io: py-pyvolve
Pyvolve is an open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution
- Homepage: https://github.com/sjspielman/pyvolve
- License: []
-
Latest release: 1.1.0
published over 3 years ago
Rankings
Maintainers (1)
Dependencies
- Biopython *
- numpy >=1.20.0
- scipy *