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rRNADif is a method to measure intragenomic 16S rRNA variability within the desired genome sequence against a chosen set of organisms. The app is calculating ML phylogenetic tree and uses mean/median branch length within a set of 16S rRNA as a measure of variability between them

Home Page: https://ostash-group.github.io/rRNADif/

License: MIT License

Shell 66.94% R 11.30% Python 21.75%
pipeline 16s phylogenetics taxonomy genomics

rrnadif's Introduction

Introduction

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DOI

rRNADif is a method to measure intragenomic 16S rRNA variability within the desired genome sequence against a chosen set of organisms. The app is calculating ML phylogenetic tree and uses mean/median branch length within set of 16S rRNA as a measure of variability between them
By default precomputed database of 21000+ fully sequenced bacterial genomes is available for comparison. However, custom database generation is possible (see documentation)
If you want to contribute, please feel free to do so !(:
Documentation and user guides are available in the website

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Citation

This is work in progress, so no publication is available at the moment. If you found this approach valuable, you can site this repo:
P. Hrab & B. Ostash 2020: rRNADif, GitHub repository: https://github.com/pavlohrab/rRNADif

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