This repository contains two R scripts (cov2clusters.R and clusteringFunctions.R) for genomic clustering and assigning cluster names of SARS-Cov-2 sequences. There is also a folder containing demo data and results.
The input is an untimed phylogenetic tree in Newick format and collection dates, either in a .csv file or .json file from a timed phylogeny. A further variable can be added into the metadata file to restrict clustering to samples sharing this feature.
To run with with default parameters and dates in a .csv file with two columns (ID, date):
cov2clusters(treeName = "tree.nwk", metafile = "dates.csv", json_dates = FALSE)
Or with a .json file for dates:
cov2clusters(treeName = "tree.nwk", json_file = "dates.json")
Please cite Sobkowiak et. al. 2022 if you choose to use this approach in published work:
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08936-4
This code has been tested on R version 3.6.0 (2019-04-26).