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https://github.com/benhid/sequoya

Solving Multiple Sequence Alignment (MSA) problems with multi-objective metaheuristics

https://github.com/benhid/sequoya

Science Score: 13.0%

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 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.3%) to scientific vocabulary

Keywords

metaheuristics msa multiple-sequence-alignment optimization python sequence-alignments
Last synced: 5 months ago · JSON representation

Repository

Solving Multiple Sequence Alignment (MSA) problems with multi-objective metaheuristics

Basic Info
  • Host: GitHub
  • Owner: benhid
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 111 MB
Statistics
  • Stars: 18
  • Watchers: 2
  • Forks: 3
  • Open Issues: 3
  • Releases: 0
Topics
metaheuristics msa multiple-sequence-alignment optimization python sequence-alignments
Created about 8 years ago · Last pushed almost 6 years ago
Metadata Files
Readme License

README.md


Logo

Solving Multiple Sequence Alignments with Python

Build Status PyPI License PyPI Python version

Sequoya is an open source software tool aimed at for solving Multiple Sequence Alignment problems with multi-objective metaheuristics.

This tool implements a distributed async version of the M2Align algorithm as shown in:

"M2Align: parallel multiple sequence alignment with a multi-objective metaheuristic". Cristian Zambrano-Vega, Antonio J. Nebro José García-Nieto, José F. Aldana-Montes. Bioinformatics, Volume 33, Issue 19, 1 October 2017, Pages 3011–3017 (DOI).

Features

  • Score functions:
    • Sum of pairs,
    • Star,
    • Minimum entropy,
    • Percentage of non-gaps,
    • Percentage of totally conserved columns,
    • STRIKE.
  • Algorithm:
    • NSGA-II,
    • Distributed NSGA-II
  • Crossover operator:
    • Single-point crossover (GapSequenceSolutionSinglePoint).
  • Mutation operators:
    • Shift closest gap group (ShiftClosedGapGroups),
    • Shift gap group (ShiftGapGroup),
    • Random gap insertion (OneRandomGapInsertion),
    • Merge two random adjacent gaps group (TwoRandomAdjacentGapGroup),
    • Multiple mutation (MultipleMSAMutation).

Install

To download and install Sequoya just clone the Git repository hosted in GitHub:

console git clone https://github.com/benhid/Sequoya.git cd Sequoya python setup.py install

Or via pip:

console pip install Sequoya

Usage

Examples of running Sequoya are located in the examples folder:

Dask distributed

For running Sequoya in a cluster of machines, first setup a network with at least one dask-cheduler node and several dask-worker nodes:

```console conda create --name dask-cluster conda activate dask-cluster

pip install git+https://github.com/benhid/Sequoya.git@develop ```

Then, on the master node run:

console dask-scheduler

On each slave node run:

console dask-worker <master-ip>:8786 --nprocs <total-cores> --nthreads 1

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: 1
Last Year
  • Watch event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 102
  • Total Committers: 4
  • Avg Commits per committer: 25.5
  • Development Distribution Score (DDS): 0.235
Top Committers
Name Email Commits
benhid m****e@h****m 78
benhid a****d@g****m 18
benhid a****b@u****s 5
Antonio J. Nebro a****o@u****m 1
Committer Domains (Top 20 + Academic)
uma.es: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 4
  • Total pull requests: 5
  • Average time to close issues: 2 days
  • Average time to close pull requests: 1 minute
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 0.25
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • 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
  • masterzhen119 (1)
  • eliotpbrenner (1)
  • Patriciatr (1)
  • MarjanHJ (1)
Pull Request Authors
  • benhid (5)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 4 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 1
  • Total maintainers: 1
pypi.org: sequoya

Solving Multiple Sequence Alignments with Python

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 4 Last month
Rankings
Dependent packages count: 10.1%
Stargazers count: 14.6%
Forks count: 19.2%
Dependent repos count: 21.6%
Average: 28.2%
Downloads: 75.4%
Maintainers (1)
benhid
Last synced: 6 months ago

Dependencies

setup.py pypi
  • bokeh ==1.1.0
  • jmetalpy ==1.5.4
  • pyMSA ==0.5.1