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    • beebop_py

      Public
      Python API for beebop
      Python
      0005Updated Dec 20, 2024Dec 20, 2024
    • PopPUNK

      Public
      PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
      Python
      Apache License 2.0
      2094252Updated Dec 20, 2024Dec 20, 2024
    • beebop

      Public
      Frontend code for beebop
      TypeScript
      Other
      0104Updated Dec 20, 2024Dec 20, 2024
    • trees_rs

      Public
      Tree inference in rust
      Rust
      GNU Affero General Public License v3.0
      1161Updated Dec 16, 2024Dec 16, 2024
    • A collection of models that can be implemented, simulated and fitted using odin, dust and mcstate.
      HTML
      Apache License 2.0
      0000Updated Dec 13, 2024Dec 13, 2024
    • Code for group website
      HTML
      Apache License 2.0
      5100Updated Dec 12, 2024Dec 12, 2024
    • Rust reimplementation of pp-sketchlib
      Rust
      Apache License 2.0
      12160Updated Dec 12, 2024Dec 12, 2024
    • An R package for translating SBML models into odin models.
      R
      0000Updated Dec 9, 2024Dec 9, 2024
    • Deploy scripts for beebop
      Python
      MIT License
      0000Updated Dec 9, 2024Dec 9, 2024
    • Methods to determine sequence element (unitig) presence/absence
      C++
      Apache License 2.0
      318120Updated Dec 6, 2024Dec 6, 2024
    • PopPIPE

      Public
      Population analysis PIPEline 🛠🧬
      Python
      Apache License 2.0
      51610Updated Dec 5, 2024Dec 5, 2024
    • ska.rust

      Public
      Split k-mer analysis – version 2
      Rust
      Apache License 2.0
      57270Updated Oct 29, 2024Oct 29, 2024
    • Pansim

      Public
      Pangenome simulator
      Rust
      MIT License
      0200Updated Oct 17, 2024Oct 17, 2024
    • ggCaller

      Public
      Bifrost graph gene caller.
      C++
      MIT License
      68840Updated Sep 20, 2024Sep 20, 2024
    • Shell
      0000Updated Sep 5, 2024Sep 5, 2024
    • readfish

      Public
      Read Until scripts with graph alignment
      Python
      GNU General Public License v3.0
      34100Updated Aug 22, 2024Aug 22, 2024
    • A viewer of odin.js models from the biomodels database
      JavaScript
      MIT License
      1110Updated Aug 8, 2024Aug 8, 2024
    • DATACIN

      Public
      Draw A Tree And Colour it IN
      Rust
      1040Updated Aug 5, 2024Aug 5, 2024
    • Mutation simulation to test ska.rust sensitivity
      Rust
      Apache License 2.0
      0100Updated Jul 24, 2024Jul 24, 2024
    • Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
      Python
      Apache License 2.0
      12230Updated Jul 22, 2024Jul 22, 2024
    • Scripts for adaptive sampling analysis
      R
      GNU General Public License v3.0
      2300Updated Jul 3, 2024Jul 3, 2024
    • Tree-free Omega Mapping By Observing Mutations of Bases and Amino acids Distributed Inside Loci
      Stan
      Apache License 2.0
      0400Updated May 22, 2024May 22, 2024
    • Library of sketching functions used by PopPUNK
      C++
      Apache License 2.0
      830100Updated Apr 15, 2024Apr 15, 2024
    • cgt

      Public
      Calculate sensible core gene thresholds for metagenomic data
      Rust
      Apache License 2.0
      0400Updated Feb 14, 2024Feb 14, 2024
    • mandrake

      Public
      Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
      Python
      Apache License 2.0
      23651Updated Dec 20, 2023Dec 20, 2023
    • This repo is for to summarise pubmed texts with a given gene/species query
      Python
      Apache License 2.0
      0000Updated Dec 11, 2023Dec 11, 2023
    • Python
      1000Updated Nov 27, 2023Nov 27, 2023
    • Backend API for the BacQuerya web app.
      Python
      Apache License 2.0
      0010Updated Sep 25, 2023Sep 25, 2023
    • BacQuerya

      Public
      Search engine for bacterial genomic information.
      JavaScript
      Apache License 2.0
      0150Updated Sep 7, 2023Sep 7, 2023
    • SimEvoNN

      Public
      Neural Network modelling for Fisher - Wright Simulation of Evolution
      Jupyter Notebook
      0020Updated Aug 29, 2023Aug 29, 2023