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adegenet

adegenet: a R package for the multivariate analysis of genetic markers

aioli

Framework for building fast genomics web tools with WebAssembly and WebWorkers

ape

:exclamation: This is a read-only mirror of the CRAN R package repository. ape — Analyses of Phylogenetics and Evolution. Homepage: http://ape-package.ird.fr/

assembly-dereplicator

A tool for removing redundant genomes from a set of assemblies

atb-ecoli

basecloud

Base R/python/etc. internal OpenStack cloud setup for Teichlab

bayespy

Bayesian Inference Tools in Python

bioconda-recipes

Conda recipes for the bioconda channel.

biowasm

WebAssembly modules for common genomics utilities

coala

A Framework for Coalescent Simulation in R

coher

covizu

Rapid analysis and visualization of coronavirus genome variation

dndscv

dN/dS methods to quantify selection in cancer and somatic evolution

docsify-static-demo

efcm_efcs_analysis

falciparum_transcriptome_manuscript

fastbaps

A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data

fastbaps_manuscript

fastq-dl

Download FASTQ files from SRA or ENA repositories.

fasttranscluster

ffpopsim

FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution. The latter is coded efficiently using Fast-Fourier Transforms to speed up recombination operations.

genesearch

global_var_manuscript

gtonkinhill.github.io

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

htsbox

My experimental tools on top of htslib. NOT OFFICIAL!!!

iq-tree

Efficient phylogenomic software by maximum likelihood

iva

de novo virus assembler of Illumina paired reads

labsite

lnaphylodyn

Package of the research: Bayesian inference on coalescent-based phylodynamics