Recombination Landscape Estimation using Recurrent Neural Networks

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

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

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

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.

AMR/VF LGT focused bacterial genomics analysis workflow

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

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

REcombination BARcode detector.

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

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

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

Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences

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

Bacterial Epigenomics Analysis SuiTe

Phasing, haplotype reconstruction and crossover detection with single-nucleotide polymorphism data from multiparental populations.

Parsimonious delimitation of large SNP datasets using the four gamete test

Recombination between heterologous human acrocentric chromosomes

This code computes the nonradiative recombination at defect centers from first-principles

view and locate recombinations positions using pedigree data

An R/C++ package for simulating the evolution of retrotransposons over time.

TopONE is a project that studies recombination events using topological data analysis. This was made in the PGC-BTIP 2024 internship by Alfonso Miguel Cruz and Claire Angelie Gabisay, and mentored by C.J. Palpal-latoc.

NMT decoding with recombination (merging).

Barycenter preserving measure reduction in JAX

Evolutionary genomics of chromosomal inversions in Atlantic herring

Tool for the visualization of recombination on chromosomes

Codes and Datasets used in the manuscript titled "Systematic Analyses of Autosomal Recombination Rates from the 1000 Genomes Project Uncovers the Global Recombination Landscape in Humans."