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

Cemracs 2018 project (CIRM, July-August 2018)

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

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

Population genetics utilities and tools

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