jbloom

SARS-CoV-2_PRJNA612766

Analysis of early Wuhan SARS-CoV-2 sequences from deleted SRA BioProject PRJNA612766

SARS2_28Dec2019_Genbank_submission

analysis of SARS-CoV-2 sequence submitted to Genbank on Dec-28-2019

epitopefinder

Python package for mapping epitopes to sequences

Huanan_market_samples

Analysis of SARS-CoV-2 read counts versus metagenomic content for Huanan Seafood market sequencing data from Chinese CDC

CoV_vs_flu_CFR

case fatality rates of COVI-19, 1918 influenza, seasonal influenza

mutpath

Map mutational paths through protein sequence space

PRJNA692319_public

Analysis of Antarctica sequencing samples contaminated with SARS-CoV-2

SARS2-clade-spike-diffs

Plot spike differences among SARS-CoV-2 Pango clades

eidith-1

⚠️ DEPRECATED ⚠️ Data is now at data.usaid.gov/Global-Health-Security-in-Development-GHSD-/PREDICT-Emerging-Pandemic-Threats-Project/tqea-hwmr

Huanan_market_samples_addtl_analysis

additional analysis of metagenomic samples from the Huanan Seafood Market

Omicron_clock

Molecular clock analysis on Omicron

SARS-CoV-2_Shen_et_al

SARS2-clock

Number of mutations relative to Wuhan-Hu-1 in SARS-CoV-2 clades

alabaster

Lightweight, configurable Sphinx theme

cluster_scripts

Scripts to investigate the SUKS cluster

COVID-19

Effect of genetic variants in COVID-19

dms_tools

redirect to package hosted on jbloomlab

DnaFeaturesViewer

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

epistasis

A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.

FluPhylogeneticsModule

High-school level educational module that uses phylogenetics to study flu

GenomeSciences541

Lectures for Genome Sciences 541

GS541-course-page

course webpage for Genome Sciences 541

GS541_epistasis_homework

demo and homework for Genome Sciences 541

huanan-environmental

mapmuts

Map mutations and infer amino-acid preferences from overlapping paired-end amino acid reads

nextstrain.org

The Nextstrain website

phyloExpCM

phylogenetic analyses with experimentally determined codon models

rebuild_Lv_SARS2_tree

Interactive phylogeny of early SARS-CoV-2 that attempts to reproduce Fig 3a of 2024 study by group of Yong-Zhen Zhang

SC2_variant_rates

analyze substitution rate and mutation behavior within variants.

snakemake

This is the development home of the workflow management system Snakemake. For general information, see