Data used in Mutational spectra distinguish SARS-CoV-2 replication niches
Each pathogen directory within this directory contains the input files used to calculate the SBS spectrum and the rescaled SBS spectrum
The sequence alignments have suffix .fasta, the rooted phylogenetic trees have suffix .nwk, the position conversion file is named conversion.txt, the reference is named reference.fasta and the SBS spectrum has suffix _SBS_spectrum.csv
The SARS-CoV-2 lineage spectra are in directory SARS-CoV-2, calculated from sequences in GISAID EPI_SET ID EPI_SET_220926yt, doi https://doi.org/10.55876/gis8.220926yt
This directory contains data used in figures. Directories contain individual READMEs with details