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SARS-CoV-2_PRJNA612766 Public
Analysis of early Wuhan SARS-CoV-2 sequences from deleted SRA BioProject PRJNA612766
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early-SARS2-trees Public
Phylogenetic analyses of early SARS-CoV-2 trees
Jupyter Notebook UpdatedMay 23, 2025 -
match_prot_to_genbank_nt Public
Match protein sequences to the closest Genbank nucleotide sequences encoding the protein
Python MIT License UpdatedMay 3, 2025 -
tree of sequences from Crits-Christoph et al (2024) paper
Python UpdatedOct 6, 2024 -
evofr Public
Forked from blab/evofrTools for evolutionary forecasting
Jupyter Notebook GNU Affero General Public License v3.0 UpdatedSep 13, 2024 -
rebuild_Lv_SARS2_tree Public
Interactive phylogeny of early SARS-CoV-2 that attempts to reproduce Fig 3a of 2024 study by group of Yong-Zhen Zhang
Jupyter Notebook UpdatedMay 20, 2024 -
SARS2-clade-spike-diffs Public
Plot spike differences among SARS-CoV-2 Pango clades
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additional analysis of metagenomic samples from the Huanan Seafood Market
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analysis of SARS-CoV-2 sequence submitted to Genbank on Dec-28-2019
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SARS2-clock Public
Number of mutations relative to Wuhan-Hu-1 in SARS-CoV-2 clades
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Huanan_market_samples Public
Analysis of SARS-CoV-2 read counts versus metagenomic content for Huanan Seafood market sequencing data from Chinese CDC
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alabaster Public
Forked from sphinx-doc/alabasterLightweight, configurable Sphinx theme
HTML Other UpdatedOct 19, 2023 -
huanan-environmental Public
Forked from sars-cov-2-origins/huanan-environmentalPython Creative Commons Zero v1.0 Universal UpdatedMar 20, 2023 -
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SC2_variant_rates Public
Forked from neherlab/SC2_variant_ratesanalyze substitution rate and mutation behavior within variants.
TeX UpdatedSep 1, 2022 -
PRJNA692319_public Public
Analysis of Antarctica sequencing samples contaminated with SARS-CoV-2
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eidith-1 Public
Forked from ecohealthalliance/eidith⚠️ DEPRECATED⚠️ Data is now at data.usaid.gov/Global-Health-Security-in-Development-GHSD-/PREDICT-Emerging-Pandemic-Threats-Project/tqea-hwmr -
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cluster_scripts Public
Forked from hodcroftlab/covariantsScripts to investigate the SUKS cluster
Python UpdatedDec 19, 2020 -
snakemake Public
Forked from snakemake/snakemakeThis is the development home of the workflow management system Snakemake. For general information, see
Python MIT License UpdatedOct 19, 2020 -
COVID-19 Public
Forked from LuChenLab/COVID-19Effect of genetic variants in COVID-19
R MIT License UpdatedMay 30, 2020 -
DnaFeaturesViewer Public
Forked from Edinburgh-Genome-Foundry/DnaFeaturesViewer👁️ Python library to plot DNA sequence features (e.g. from Genbank files)
Python Other UpdatedApr 10, 2020 -
CoV_vs_flu_CFR Public
case fatality rates of COVI-19, 1918 influenza, seasonal influenza
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nextstrain.org Public
Forked from nextstrain/nextstrain.orgThe Nextstrain website
JavaScript UpdatedJan 26, 2020 -
GS541_epistasis_homework Public
demo and homework for Genome Sciences 541
Jupyter Notebook UpdatedJun 6, 2019 -
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epistasis Public
Forked from harmslab/epistasisA Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
Python The Unlicense UpdatedNov 5, 2018 -
mapmuts Public
Map mutations and infer amino-acid preferences from overlapping paired-end amino acid reads
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