Journal article

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments

David Edwards, Sebastián Duchêne, Bernard Pope, Kathryn Holt

Cold Spring Harbor Laboratory | Published : 2020

Abstract

Abstract Homoplasic single nucleotide polymorphisms (SNPs) are considered important signatures of strong (positive) selective pressure, and hence of adaptive evolution for clinically relevant traits such as antibiotic resistance and virulence. Here we present a new tool, SNPPar, for efficient detection and analysis of homoplasic SNPs from large WGS datasets (>1,000 isolates and/or >100,000 SNPs). SNPPar takes as input a SNP alignment, tree and annotated reference genome, and uses a combination of simple monophyly tests and ancestral state reconstruction (ASR, via TreeTime) to assign mutation events to branches and identify homoplasies. Mutations are annotated at the level of codon and gene, ..

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