Resources

Fasta SNV Caller – a simple way to call SNPs from high-quality (read: long, overlapping, low-structural-divergence) fastas (e.g. isolate assemblies). Managed by Peter Laurin

Haplotype Visualizer – This repo provides an R script to construct ‘haplotype plots’ of genetic variation in a genomic window, using delimited files or numpy arrays of genetic variants.

A hard sweep reaching 50% frequency, with descending haplotypes sorted by nucleotide divergence from the most-frequent haplotype. Red denotes deleterious variants, while blue denotes neutral variants.