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Open Source Science

https://github.com/benhid/pymsa

Scoring multiple sequence alignments with Python

https://github.com/benhid/pymsa

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.3%) to scientific vocabulary

Keywords

entropy fasta gaps msa python score sequence-alignment sumofpairs
Last synced: 5 months ago · JSON representation

Repository

Scoring multiple sequence alignments with Python

Basic Info
  • Host: GitHub
  • Owner: benhid
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 1.34 MB
Statistics
  • Stars: 23
  • Watchers: 3
  • Forks: 10
  • Open Issues: 5
  • Releases: 1
Topics
entropy fasta gaps msa python score sequence-alignment sumofpairs
Created over 8 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md


pyMSA

Scoring Multiple Sequence Alignments with Python

Build Status PyPI License PyPI Python version

pyMSA is an open source software tool aimed at providing a number of scores for multiple sequence alignment (MSA) problems. A tutorial about pyMSA is available in the resources folder of the proyect.

Features

Score functions implemented:

  • Sum of pairs,
  • Star,
  • Minimum entropy,
  • Percentage of non-gaps,
  • Percentage of totally conserved columns and
  • STRIKE (Single sTRucture Induced Evaluation).

Downloading

To download PyMSA just clone the Git repository hosted in GitHub: bash $ git clone https://github.com/benhid/pyMSA.git $ python setup.py install

Alternatively, you can install it with pip: bash $ pip install pyMSA

Usage

An example of running all the included scores is located in the example folder.


Terminal session

Authors

Active development team

License

This project is licensed under the terms of the MIT - see the LICENSE file for details.

Owner

  • Name: Antonio
  • Login: benhid
  • Kind: user
  • Location: Málaga, Spain
  • Company: University of Málaga

Software / DevOps Engineer and Researcher @KhaosResearch

GitHub Events

Total
  • Watch event: 3
Last Year
  • Watch event: 3

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 6
  • Average time to close issues: 22 minutes
  • Average time to close pull requests: 1 minute
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 1.75
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • multimeric (3)
  • HodaFakharzade (1)
Pull Request Authors
  • benhid (6)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 97 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 5
  • Total maintainers: 1
pypi.org: pymsa

Scoring Multiple Sequence Alignments with Python

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 97 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 11.4%
Stargazers count: 13.7%
Average: 14.4%
Downloads: 15.1%
Dependent repos count: 21.5%
Maintainers (1)
benhid
Last synced: 6 months ago

Dependencies

setup.py pypi