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metabolishmm

Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs

https://github.com/elizabethmcd/metabolishmm

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: biorxiv.org
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs

Basic Info
  • Host: GitHub
  • Owner: elizabethmcd
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 25.7 MB
Statistics
  • Stars: 18
  • Watchers: 2
  • Forks: 5
  • Open Issues: 10
  • Releases: 0
Created over 7 years ago · Last pushed over 4 years ago
Metadata Files
Readme License

README.md




PyPI version

metabolisHMM: a tool for exploration of microbial phylogenies and metabolic pathways

metabolisHMM is a pipeline for visualizing the distribution and evolutionary relationships using curated and custom Hidden Markov Model (HMM) profiles. Functional annotation of microbial genomes using HMMs is becoming increasingly popular over BLAST-based methods, however methods for rapidly visualizing and summarizing these results are lacking. This software automates the process of searching any set of metabolic markers that have an HMM profile against a set of genomes, and outputs phylogenies, summary statistics, and heatmap presence/absence visualizations. The metabolisHMM software is written in python and is available on PyPi.

Please see the wiki for installation and usage instructions.

If you find metabolisHMM useful for your research, please cite the biorXiv preprint as:

McDaniel, E.A., Anantharaman, K., McMahon, K.D. 2019. metabolisHMM: Phylogenomic analysis for exploration of microbial phylogenies and metabolic pathways. bioRxiv. 2019.12.20.884627

Owner

  • Name: Elizabeth McDaniel
  • Login: elizabethmcd
  • Kind: user
  • Location: Berkeley, CA
  • Company: Arcadia Science

Scientist @ Arcadia Science developing computational pipelines.

GitHub Events

Total
  • Issues event: 1
  • Issue comment event: 1
Last Year
  • Issues event: 1
  • Issue comment event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 180
  • Total Committers: 2
  • Avg Commits per committer: 90.0
  • Development Distribution Score (DDS): 0.006
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Elizabeth McDaniel e****l@w****u 179
elizabethmcd e****l@k****l 1
Committer Domains (Top 20 + Academic)
wisc.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 60
  • Total pull requests: 1
  • Average time to close issues: 27 days
  • Average time to close pull requests: N/A
  • Total issue authors: 13
  • Total pull request authors: 1
  • Average comments per issue: 1.73
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • 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
View more stats
Top Authors
Issue Authors
  • elizabethmcd (47)
  • Streptomyces1 (2)
  • bbaker567 (1)
  • Thexiyang (1)
  • nikobiota (1)
  • morgvevans (1)
  • mohitsharma-123 (1)
  • thatch (1)
  • Binvir (1)
  • susheelbhanu (1)
  • taylorreiter (1)
  • sarah872 (1)
  • vinisalazar (1)
Pull Request Authors
  • thatch (1)
Top Labels
Issue Labels
bug (1) enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 31 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 6
  • Total maintainers: 1
pypi.org: metabolishmm

Constructing phylogenies and performing functional annotations with HMM markers

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 31 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 14.2%
Stargazers count: 14.5%
Average: 18.5%
Dependent repos count: 21.7%
Downloads: 32.0%
Maintainers (1)
elizabethmcd93
Last synced: 11 months ago

Dependencies

data/requirements 2.txt pypi
  • biopython *
  • matplotlib *
  • numpy *
  • pandas *
  • seaborn *
requirements.txt pypi
  • biopython *
  • matplotlib *
  • numpy *
  • pandas *
  • seaborn *