HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

Horizontal gene transfer (HGT) identification pipeline

HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.

Automatic evaluation of HGTs

Rapid and simple taxonomic profiling of genome and metagenome contigs

An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences

A pipeline to investigate horizontal gene transfer from NGS data

codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, prophage, etc.) relative to the full genome.

A novel bioinformatics pipeline for recent horizontal gene transfer detecting.

A simulator for horizontal gene transfer (HGT) in microbial communities

Simulator for species and gene trees with asymmetric evolution rates

Cemracs 2018 project (CIRM, July-August 2018)

TrIdent- Transduction Identification: Automatic detection, classification and characterization of active transduction events in microbiomes.

This is a metagenomics pipeline to detect phages and Auxiliary Metabolic Genes (AMGs) from specific virtual genomes of bacteria (MAGs) in the human microbiome.

Script repository related to the data processing and analyses of the study: "Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes".

Population genetics utilities and tools

Official website of the Burstein Lab at Tel Aviv University - computational microbiology using NLP, machine learning, and large language models to study CRISPR-Cas systems, antimicrobial resistance, horizontal gene transfer, and microbial interactions

This repository provides the code to screen de novo assembled ant genome assemblies for bacterial and other sources of contamination.

Graph-based methods for detecting horizontal gene transfer (HGT) candidates in bacterial proteomes using sequence similarity and network analysis, developed for HUJI’s Algorithms in Computational Biology course (76558)

In silico structural predictions and analysis for Rinke et al. 2026, "Comparative analysis of 163 ant genomes reveals recurrent horizontal gene transfer from bacteria to ants"