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Prokaryotic Recombination Dashboard


NimwegenLab

Bowtie2 documentation
PhyML documentation
reference genomes genome fragments/sequence reads
 

RECOPHY provides a range of summary statistics , such as the fraction of SNPs supporting each branch, the fraction of clonal and recombined genome between each pair of strains and the level of population structure. Examples with detailed explanation were presented in the eLife paper "Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species" Thomas Sakoparnig, Chris Field, Erik van Nimwegen; Elife, 2021.

The user typically uploads one or more reference genomes and a number of query genomes as either finished genomes or raw next generation sequencing data. The pipeline uses REALPHY to construct a multiple sequence core alignment and then a number of summary statistics is computed. This can take, depending on the size of the data, from several hours to a several days. Afterwards these statistics can be explored on this interactive website.

Citation:

Thomas Sakoparnig, Chris Field, Erik van Nimwegen Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species. Elife, 2021

Terms of use

The developers of the RECOPHY give permission to you and your institution to use the RECOPHY webserver for internal, research purposes, on the following conditions:

  1. The RECOPHY webserver will be used by you and/or your institution solely for non-commercial purposes, except with express permission from the authors.
  2. You may provide us with feedback on the use of the RECOPHY webserver in your research, and we are permitted to use any information you provide in making changes to RECOPHY.
  3. Any risk associated with using the RECOPHY webserver is with you and your institution.
  4. Any results produced with RECOPHY are licenced under CC BY-NC 4.0 .
  5. The RECOPHY webserver should be cited in any publication(s) reporting on data obtained by using it as:

    Thomas Sakoparnig, Chris Field and Erik van Nimwegen Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species. eLife, Jan 8 2021

Commercial users should contact us for licensing arrangements.

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