IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

discoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples

Recombination Landscape Estimation using Recurrent Neural Networks

Inferring bacterial recombination rates from large-scale sequencing datasets.

SNPbinner is a utility for the generation of genotype crossover points and binmaps based on SNP data across recombinant inbred lines.

compare sequences to a shared root reference sequence.

Reproducible workflow for SARS-CoV-2 recombinant sequence detection.

Using correlated substitutions to infer recombination rates in RNA viruses

AMR/VF LGT focused bacterial genomics analysis workflow

Monte Carlo codes to simulate polar domains in hybrid perovskite solar cells

Implementation of Semantic Parsing with BERT and compositional pre-training on GeoQuery

TreeKnit is a package that infers Ancestral Reassortment Graphs for segmented genomes (typically, human influenza).

REcombination BARcode detector.

Bacterial Epigenomics Analysis SuiTe

Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences

HTML5 pedigree/haplotype explorer, featuring a rich selection of comparison tools.

A computational framework for tetrad-based genotyping & recombination landscape analysis

Recombination between heterologous human acrocentric chromosomes

Parsimonious delimitation of large SNP datasets using the four gamete test