Evolutionary Bioinformatics Tools

Repositories

• Taiwan-COVID-19-2021

  Data, methods, and results of analyses tracking the May 2021 COVID-19 outbreak in Taiwan.

  visualization r taiwan epidemiology covid-19 sars-cov-2
  R GPL-3.0 0 2 0 0 Updated May 31, 2021

• SNPGenie

  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

  evolution perl next-generation-sequencing vcf population-genetics dnds-estimation molecular-evolution
  Perl GPL-3.0 28 64 15 0 Updated May 26, 2021

• SARS-CoV-2-ORF3d

  Supplementary scripts for Nelson et al. (2020) paper on ORF3d

  python r perl biopython overlapping-genes within-host covid-19
  R GPL-3.0 3 3 0 0 Updated Nov 5, 2020

• trevolver

  Program for simulating non-reversible DNA sequence evolution on a fixed bifurcating tree using trinucleotide context

  simulation evolution perl mutation phylogenetic-trees dna molecular-evolution
  Perl GPL-3.0 1 6 0 0 Updated Sep 19, 2020

• OLGenie

  Program for estimating dN/dS in overlapping genes (OLGs)

  perl selection overlapping dnds-estimation molecular-evolution positive-selection dnds
  Perl GPL-3.0 2 6 0 0 Updated Sep 19, 2020

• EBT

  Evolutionary Bioinformatics Toolkit (EBT)

  perl vcf fasta gtf sequence dna-sequences sequence-alignment
  Perl GPL-3.0 3 8 0 0 Updated Jul 14, 2020