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@bacpop Bacterial population genetics

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    40 repositories

    • compartmental-models-odin-dust

      Public
      A collection of models that can be implemented, simulated and fitted using odin, dust and mcstate.
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • ska.rust

      Public
      Split k-mer analysis – version 2
      bioinformaticsalignmentsequencek-merskarust
      Rust
      •
      Apache License 2.0
      •5•73•6•1•Updated Jan 28, 2025Jan 28, 2025

    • beebop

      Public
      Frontend code for beebop
      TypeScript
      •
      Other
      •0•1•0•3•Updated Jan 28, 2025Jan 28, 2025

    • beebop_py

      Public
      Python API for beebop
      Python
      •0•0•0•4•Updated Jan 28, 2025Jan 28, 2025

    • Pansim

      Public
      Pangenome simulator
      Rust
      •
      MIT License
      •0•2•0•0•Updated Jan 27, 2025Jan 27, 2025

    • PopPUNK

      Public
      PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
      genomicssketchingbacteriak-merpopulation-genetics
      Python
      •
      Apache License 2.0
      •20•93•26•2•Updated Jan 27, 2025Jan 27, 2025

    • sketchlib.rust

      Public
      Rust reimplementation of pp-sketchlib
      Rust
      •
      Apache License 2.0
      •2•3•17•0•Updated Jan 27, 2025Jan 27, 2025

    • odinviewer

      Public
      A viewer of odin.js models from the biomodels database
      JavaScript
      •
      MIT License
      •1•1•1•0•Updated Jan 23, 2025Jan 23, 2025

    • PopPIPE

      Public
      Population analysis PIPEline 🛠🧬
      Python
      •
      Apache License 2.0
      •6•16•1•0•Updated Jan 23, 2025Jan 23, 2025

    • pp-sketchlib

      Public
      Library of sketching functions used by PopPUNK
      C++
      •
      Apache License 2.0
      •8•30•11•0•Updated Jan 6, 2025Jan 6, 2025

    • trees_rs

      Public
      Tree inference in rust
      Rust
      •
      GNU Affero General Public License v3.0
      •1•1•6•0•Updated Jan 6, 2025Jan 6, 2025

    • bacpop-website

      Public
      Code for group website
      bioinformaticsmodellingbacteriapopulation-genetics
      HTML
      •
      Apache License 2.0
      •5•1•0•0•Updated Dec 12, 2024Dec 12, 2024

    • SBMLtoOdin

      Public
      An R package for translating SBML models into odin models.
      R
      •0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

    • beebop-deploy

      Public
      Deploy scripts for beebop
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

    • unitig-caller

      Public
      Methods to determine sequence element (unitig) presence/absence
      C++
      •
      Apache License 2.0
      •3•18•12•0•Updated Dec 6, 2024Dec 6, 2024

    • ggCaller

      Public
      Bifrost graph gene caller.
      C++
      •
      MIT License
      •6•91•3•0•Updated Sep 20, 2024Sep 20, 2024

    • beebop-k8s

      Public
      Shell
      •0•0•0•0•Updated Sep 5, 2024Sep 5, 2024

    • readfish

      Public
      Read Until scripts with graph alignment
      Python
      •
      GNU General Public License v3.0
      •35•1•0•0•Updated Aug 22, 2024Aug 22, 2024

    • DATACIN

      Public
      Draw A Tree And Colour it IN
      Rust
      •1•0•4•0•Updated Aug 5, 2024Aug 5, 2024

    • ska_simulations

      Public
      Mutation simulation to test ska.rust sensitivity
      Rust
      •
      Apache License 2.0
      •0•1•0•0•Updated Jul 24, 2024Jul 24, 2024

    • CELEBRIMBOR

      Public
      Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
      metagenomicsbioinfomaticspangenomes
      Python
      •
      Apache License 2.0
      •1•22•3•0•Updated Jul 22, 2024Jul 22, 2024

    • adaptive_sampling_scripts

      Public
      Scripts for adaptive sampling analysis
      R
      •
      GNU General Public License v3.0
      •2•3•0•0•Updated Jul 3, 2024Jul 3, 2024

    • TOMBOMBADIL

      Public
      Tree-free Omega Mapping By Observing Mutations of Bases and Amino acids Distributed Inside Loci
      Stan
      •
      Apache License 2.0
      •0•4•0•0•Updated May 22, 2024May 22, 2024

    • cgt

      Public
      Calculate sensible core gene thresholds for metagenomic data
      Rust
      •
      Apache License 2.0
      •0•4•0•0•Updated Feb 14, 2024Feb 14, 2024

    • mandrake

      Public
      Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
      genomicsembeddingpathogensgpucuda
      Python
      •
      Apache License 2.0
      •2•36•5•1•Updated Dec 20, 2023Dec 20, 2023

    • Bacquerya-LLM

      Public
      This repo is for to summarise pubmed texts with a given gene/species query
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 11, 2023Dec 11, 2023

    • genesearch

      Public
      Python
      •1•0•0•0•Updated Nov 27, 2023Nov 27, 2023

    • BacQuerya-api

      Public
      Backend API for the BacQuerya web app.
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated Sep 25, 2023Sep 25, 2023

    • BacQuerya

      Public
      Search engine for bacterial genomic information.
      search-enginegenomicsbacteria
      JavaScript
      •
      Apache License 2.0
      •0•1•5•0•Updated Sep 7, 2023Sep 7, 2023

    • SimEvoNN

      Public
      Neural Network modelling for Fisher - Wright Simulation of Evolution
      Jupyter Notebook
      •0•0•2•0•Updated Aug 29, 2023Aug 29, 2023