This repository contains the datasets and RMarkdown files to reproduce the results described in the article "Genomic epidemiology and evolution of rhinovirus in western Washington State, 2021-22".

FUBAR-selection: includes the results of the selection pressure inferred with the method FUBAR. This method infers nonsynoymous (dN) and synonymous (dS) substitution rates on a per-site basis for the polyprotein coding alignment and the corresponding phylogeny.

MEGA-IQTREE: contains the phylogenetic trees of the VP-1 region of RV-A, RV-B and RV-C inferred by neighbor joining method with MEGA and maximum likelihood with IQ-TREE

PCA: code and datasets to reproduce the principal component analysis (PCA) and hierarchical clustering described in the article

Phylogenetic-trees: constructed trees with VP1 and 3D region of RV-A, RV-B and RV-C species

RV_statistics: code and datasets to reproduce the charactrization of species and genotype seasonality and the association study with epidemiological characteristics of the individuals described in the article

Rarefaction: code and datasets to reproduce the rarefaction and extrapolation curves used to evaluate the RV genotype diversity