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phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

https://github.com/biobakery/phylophlan

Science Score: 39.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.2%) to scientific vocabulary

Keywords

biobakery phylogenetic-trees python tools

Keywords from Contributors

metagenomics public bioinformatics circular-visualization taxonomic-trees gene-composition microbiome pangenome
Last synced: 6 months ago · JSON representation

Repository

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

Basic Info
Statistics
  • Stars: 151
  • Watchers: 5
  • Forks: 35
  • Open Issues: 51
  • Releases: 7
Topics
biobakery phylogenetic-trees python tools
Created about 6 years ago · Last pushed 8 months ago
Metadata Files
Readme License

readme.md

PhyloPhlAn

PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. PhyloPhlAn can assign both genomes and metagenome-assembled genomes (MAGs) to species-level genome bins (SGBs). PhyloPhlAn can reconstruct strain-level phylogenies using clade-specific maximally informative phylogenetic markers, and can also scale to very-large phylogenies comprising >17,000 microbial species.

Installation

Bioconda

You can install PhyloPhlAn using conda as follows:

~~~Bash conda install -c bioconda phylophlan ~~~

Repository

You can clone the PhyloPhlAn repository from GitHub:

~~~Bash git clone https://github.com/biobakery/phylophlan cd phylophlan python setup.py install ~~~

Then remember to check that the Dependencies and Tools are in stalled and available in your system.

Tutorials

Support

We provide support through the bioBakery help forum and through the issues tracking system of the PhyloPhlAn repository.

Citation

If you used PhyloPhlAn please cite the following paper:

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
Francesco Asnicar, Andrew Maltez Thomas, Francesco Beghini, Claudia Mengoni, Serena Manara, Paolo Manghi, Qiyun Zhu, Mattia Bolzan, Fabio Cumbo, Uyen May, Jon G. Sanders, Moreno Zolfo, Evguenia Kopylova, Edoardo Pasolli, Rob Knight, Siavash Mirarab, Curtis Huttenhower, and Nicola Segata
Nat Commun 11, 2500 (2020)
DOI: https://doi.org/10.1038/s41467-020-16366-7

Owner

  • Name: bioBakery
  • Login: biobakery
  • Kind: organization

Software, documentation, and tutorials for microbial community profiling.

GitHub Events

Total
  • Issues event: 2
  • Watch event: 28
  • Issue comment event: 2
  • Push event: 10
  • Fork event: 1
Last Year
  • Issues event: 2
  • Watch event: 28
  • Issue comment event: 2
  • Push event: 10
  • Fork event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 457
  • Total Committers: 16
  • Avg Commits per committer: 28.563
  • Development Distribution Score (DDS): 0.197
Past Year
  • Commits: 13
  • Committers: 2
  • Avg Commits per committer: 6.5
  • Development Distribution Score (DDS): 0.077
Top Committers
Name Email Commits
Francesco Asnicar 5****r 367
nsegata n****a@l****t 23
Claudia Mengoni 4****i 15
Michal Puncochar m****r@g****m 14
MattiaBo m****7@g****m 11
Katarina Mladenovic k****c@g****m 6
Katarina Mladenovic 8****t 5
Francesco Beghini f****i@u****t 3
Hocnonsense 4****e 2
Nicola Segata n****a@u****t 2
abmiguez b****z@g****m 2
Sagun Maharjan s****0@h****m 2
paolo.manghi p****i@s****t 2
Kenzo-Hugo Hillion h****o@p****t 1
Thomas Kuntz t****h@g****m 1
fabio-cumbo f****o@g****m 1
Committer Domains (Top 20 + Academic)
unitn.it: 2 posteo.net: 1 studio.unibo.it: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 105
  • Total pull requests: 7
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 2 months
  • Total issue authors: 84
  • Total pull request authors: 6
  • Average comments per issue: 3.54
  • Average comments per pull request: 1.43
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 3
  • Pull request authors: 0
  • Average comments per issue: 0.67
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • LisaCarraro (4)
  • ganiatgithub (4)
  • EricDeveaud (3)
  • fujch7 (3)
  • pavlo888 (3)
  • adityabandla (3)
  • llk578496 (3)
  • gunturus (2)
  • jiaojiaoguan (2)
  • Hocnonsense (2)
  • catcatzilla (2)
  • zckoo007 (2)
  • fancyge (1)
  • Valentin-Bio (1)
  • Jimmyeric94 (1)
Pull Request Authors
  • kaca-git (2)
  • Hocnonsense (2)
  • nick-youngblut (1)
  • cumbof (1)
  • alexhbnr (1)
  • khillion (1)
Top Labels
Issue Labels
bug (10) question (4) good first issue (3) enhancement (2) help wanted (2) documentation (1)
Pull Request Labels
enhancement (2)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 704 last-month
  • Total dependent packages: 2
    (may contain duplicates)
  • Total dependent repositories: 3
    (may contain duplicates)
  • Total versions: 8
  • Total maintainers: 2
pypi.org: phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

  • Versions: 6
  • Dependent Packages: 1
  • Dependent Repositories: 3
  • Downloads: 704 Last month
Rankings
Dependent packages count: 4.8%
Stargazers count: 7.1%
Forks count: 7.1%
Average: 7.9%
Dependent repos count: 9.0%
Downloads: 11.4%
Maintainers (1)
biobakery
Last synced: 6 months ago
spack.io: py-phylophlan

PhyloPhlAn 3.0 is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.

  • Versions: 2
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Average: 16.6%
Forks count: 18.9%
Stargazers count: 19.6%
Dependent packages count: 28.1%
Maintainers (1)
adamjstewart
Last synced: 6 months ago

Dependencies

.github/workflows/python-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
setup.py pypi