Bacterial population genetics

ggCaller

Bifrost graph gene caller.

PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

ska.rust

Split k-mer analysis – version 2

mandrake

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

pp-sketchlib

Library of sketching functions used by PopPUNK

unitig-caller

Methods to determine sequence element (unitig) presence/absence

unitig-counter

Uses cDBG to count unitigs in bacterial populations

PopPIPE

Population analysis PIPEline 🛠🧬

CELEBRIMBOR

Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs

SKA2

Split Kmer Analysis - version 2

CELEBRIMBOR_stan

cgt

Calculate sensible core gene thresholds for metagenomic data

Pansim

Pangenome simulator

TOMBOMBADIL

Tree-free Omega Mapping By Observing Mutations of Bases and Amino acids Distributed Inside Loci

BacQuerya

Search engine for bacterial genomic information.

beebop

Frontend code for beebop

ska_simulations

Mutation simulation to test ska.rust sensitivity

trees_rs

Tree inference in rust

BacQuerya-api

Backend API for the BacQuerya web app.

bacpop-website

Code for group website

Bacquerya-LLM

This repo is for to summarise pubmed texts with a given gene/species query

beebop-deploy

Deploy scripts for beebop

beebop_data

Lineage databases for beebop_py tests

beebop_py

Python API for beebop

compartmental-models-odin-dust

A collection of models that can be implemented, simulated and fitted using odin, dust and mcstate.

DATACIN

Draw A Tree And Colour it IN

genesearch

pp-netlib

Network tools for PopPUNK

SBMLtoOdin

An R package for translating SBML models into odin models.

SimEvoNN

Neural Network modelling for Fisher - Wright Simulation of Evolution