https://github.com/norwegianveterinaryinstitute/alppaca

A tooL for Prokaryotic Phylogeny And Clustering Analysis
https://github.com/norwegianveterinaryinstitute/alppaca

clustering nextflow phylogeny pipeline

Last synced: 5 months ago
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A tooL for Prokaryotic Phylogeny And Clustering Analysis

• Host: GitHub
• URL: https://github.com/norwegianveterinaryinstitute/alppaca
• Owner: NorwegianVeterinaryInstitute
• License: bsd-3-clause
• Created: 2020-08-14T07:04:58.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2025-07-28T09:40:30.000Z (11 months ago)
• Last Synced: 2025-10-24T01:45:14.474Z (8 months ago)
• Topics: clustering, nextflow, phylogeny, pipeline
• Language: Nextflow
• Homepage:
• Size: 52.7 MB
• Stars: 13
• Watchers: 1
• Forks: 4
• Open Issues: 8
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

          
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7331351.svg)](https://doi.org/10.5281/zenodo.7331351)

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# Information

ALPPACA is a pipeline for various phylogenetic analyses of prokaryotic isolates. 

The pipeline includes core genome-, core gene-, and reference-based (mapping) phylogeny, as well as FastANI and cgMLST (under development). 

Please see the [description](https://github.com/NorwegianVeterinaryInstitute/ALPPACA/wiki/1.-Pipeline-and-program-descriptions) page for more information.

# Installation and Running

Please check the [wiki](https://github.com/NorwegianVeterinaryInstitute/ALPPACA/wiki).

- [Installation](https://github.com/NorwegianVeterinaryInstitute/ALPPACA/wiki/2.-Installation)

- [How to run](https://github.com/NorwegianVeterinaryInstitute/ALPPACA/wiki/3.-Input-and-usage)

- [Output file descriptions](https://github.com/NorwegianVeterinaryInstitute/ALPPACA/wiki/5.-Output-files)

# Citation

ALPPACA has been published in Journal of Open Source Software. Use the following citation:

Kaspersen et al., (2022). ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis. Journal of Open Source Software, 7(79), 4677, https://doi.org/10.21105/joss.04677