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bioconda-recipes Public
Forked from bioconda/bioconda-recipesConda recipes for the bioconda channel.
Shell MIT License UpdatedMay 28, 2025 -
BTE Public
Cython API for the Mutation Annotated Tree (MAT) Online Phylogenetics Toolkit
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automated-lineage-json Public
Streamlit webapp for the annotation of Nextstrain Auspice v2 JSON with lineage labels based on genotype representation.
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xtts-api-server Public
Forked from daswer123/xtts-api-serverA simple FastAPI Server to run XTTSv2
Python MIT License UpdatedJan 30, 2024 -
lineage-manuscript Public
Notebooks and materials for manuscript results replication.
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LLMChat Public
Forked from hc20k/LLMChatA Discord chatbot that supports popular LLMs for text generation and ultra-realistic voices for voice chat.
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oobabot Public
Forked from chrisrude/oobabotA Discord bot which talks to Large Language Model AIs running on oobabooga's text-generation-webui
Python MIT License UpdatedOct 19, 2023 -
genslm Public
Forked from ramanathanlab/genslmGenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics
Python MIT License UpdatedJul 18, 2023 -
citation_llm Public
Repository containing code exploring the use of citation context information extracted from academic and scientific work for Retrieval-Augmented Generation (RAG).
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matutils_benchmarking Public
Forked from bpt26/matutils_benchmarkingFiles used for comparing the performance of matUtils to related tools
Shell UpdatedMay 30, 2023 -
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usher Public
Forked from yatisht/usherUltrafast Sample Placement on Existing Trees
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autolin Public
Repository containing a method for automatically identifying pathogen lineages from a phylogeny.
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pathogen-protobuf Public
Short pipeline to create MAT Protobuf (.pb) files from Genbank (.gb) or fasta format files.
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corbett-lab.github.io Public
Forked from corbett-lab/corbett-lab.github.ioHTML MIT License UpdatedApr 28, 2023 -
influenza-mat Public
Code and information for constructing influenzavirus Mutation Annotated Trees (MATs)
Python GNU General Public License v3.0 UpdatedMar 30, 2023 -
auto-pango-designation Public
Forked from cov-lineages/pango-designationRepository for automated flagging of new lineages for pango designation.
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introduction-website Public
Code for a webpage displaying introductions and resulting clusters of coronavirus across the USA.
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pango_aliasor Public
Forked from corneliusroemer/pango_aliasorUtility to alias and dealias pango lineages
Python MIT License UpdatedFeb 22, 2023 -
parsevcf Public
Forked from lilymaryam/parsevcfConvert VCF to Diff format variant files.
Python MIT License UpdatedFeb 12, 2023 -
pango-sequences Public
Forked from corneliusroemer/pango-sequencesConsensus sequences for each Pango lineage
Python UpdatedFeb 1, 2023 -
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pandemic-simulator Public
Workflows and files for simulation of SARS-CoV-2-like pandemic data
Python UpdatedJan 25, 2023 -
cluster-heuristic Public
Repository containing code for analyzing global SARS-CoV-2 transmission for publication.
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cov2-selection Public
Scripts for analysis of purifying selection across SARS-CoV-2 genes using global phylogenies.
Python UpdatedJan 17, 2023 -
timeseries-lineage-analysis Public
Repository containing scripts and data for the analysis of the persistence and growth of arbitrary lineage annotations for SARS-CoV-2 over a series of public phylogenies.
Jupyter Notebook UpdatedJan 4, 2023 -
VGsim Public
Forked from Genomics-HSE/VGsimVGsim is a fast and scalable simulator of viral genealogies during global pandemic.
Cython GNU General Public License v3.0 UpdatedDec 6, 2022 -
bte-binder Public
A jupyter Binder repository containing documentation and example analyses for Big Tree Explorer (BTE)
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somatic-mutation-analysis Public
Pipeline and scripts for downstream analysis on somatic mutation data obtained with Circleseq
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