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auto-pango-designation

Repository for automated flagging of new lineages for pango designation.

autolin

Repository containing a method for automatically identifying pathogen lineages from a phylogeny.

automated-lineage-json

Streamlit webapp for the annotation of Nextstrain Auspice v2 JSON with lineage labels based on genotype representation.

basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

bin

Various unsorted scripts and tools related to various projects

bioconda-recipes

Conda recipes for the bioconda channel.

breakpoint-assembly

breakpoint_analysis

bte

Cython API for the Mutation Annotated Tree (MAT) Online Phylogenetics Toolkit

bte-benchmark

Repository of scripts used to benchmark BTE.

bte-binder

A jupyter Binder repository containing documentation and example analyses for Big Tree Explorer (BTE)

circleseq

Primary analysis pipeline for ultra-accurate sequencing data

citation_llm

Repository containing code exploring the use of citation context information extracted from academic and scientific work for Retrieval-Augmented Generation (RAG).

cluster-heuristic

Repository containing code for analyzing global SARS-CoV-2 transmission for publication.

cool_encoder

corbett-lab.github.io

cov2-selection

Scripts for analysis of purifying selection across SARS-CoV-2 genes using global phylogenies.

galago

Interpretation aids for genomic epidemiology

genslm

GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics

helmsman

highly-efficient & lightweight mutation signature matrix aggregation

hybrid_expression

Scripts and pipeline for phasing of long-read expression data from interspecific hybrids.

influenza-mat

Code and information for constructing influenzavirus Mutation Annotated Trees (MATs)

introduction-website

Code for a webpage displaying introductions and resulting clusters of coronavirus across the USA.

lineage-manuscript

Notebooks and materials for manuscript results replication.

llmchat

A Discord chatbot that supports popular LLMs for text generation and ultra-realistic voices for voice chat.

matgui

Streamlit webapp for generation of Nextstrain JSON from the global SARS-CoV-2 phylogeny.

matutils_benchmarking

Files used for comparing the performance of matUtils to related tools

oobabot

A Discord bot which talks to Large Language Model AIs running on oobabooga's text-generation-webui

pandemic-simulator

Workflows and files for simulation of SARS-CoV-2-like pandemic data

pango-sequences

Consensus sequences for each Pango lineage