An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
☆27Aug 8, 2022Updated 3 years ago
Alternatives and similar repositories for GeneMates
Users that are interested in GeneMates are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Searching for Horizontal Gene Transfer☆10Feb 22, 2020Updated 6 years ago
- A novel bioinformatics pipeline for recent horizontal gene transfer detecting.☆12Nov 13, 2018Updated 7 years ago
- ☆38Apr 14, 2022Updated 4 years ago
- Program for finding horizontal gene transfer using BLAST result☆11May 26, 2023Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Feb 3, 2021Updated 5 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasm…☆52Feb 2, 2021Updated 5 years ago
- A simulator for horizontal gene transfer (HGT) in microbial communities☆10Oct 5, 2020Updated 5 years ago
- ☆13Sep 4, 2017Updated 8 years ago
- transposable element typing pipeline☆19Mar 8, 2024Updated 2 years ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆45Aug 20, 2025Updated 8 months ago
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆86Jan 24, 2026Updated 3 months ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆14Aug 26, 2024Updated last year
- Bioinformatics tool to find integrons in bacterial genomes☆87May 7, 2025Updated 11 months ago
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆13Jun 10, 2021Updated 4 years ago
- Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.☆121Jan 22, 2025Updated last year
- A simple-to-use tool for visualizing and comparing genome contexts for numerous genomes☆18Dec 1, 2025Updated 5 months ago
- Horizontal gene transfer (HGT) identification pipeline☆71May 17, 2023Updated 2 years ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆98Dec 9, 2025Updated 4 months ago
- A microbial genomic analysis pipeline used by the Djordjevic Lab☆13Feb 9, 2025Updated last year
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆216Aug 27, 2025Updated 8 months ago
- rhierbaps: R implementation of hierBAPS☆36Feb 23, 2026Updated 2 months ago
- An updated pipeline for pangenome investigation☆356Apr 22, 2026Updated 2 weeks ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Whole genome core alignments from multiple draft genomes☆13Sep 14, 2016Updated 9 years ago
- An easy way of MLSTyping your genomes in R.☆19Dec 21, 2020Updated 5 years ago
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆64Updated this week
- A simple program for evaluate the assembly of a give genome.☆18Mar 3, 2023Updated 3 years ago
- GenoVi, an automated customizable circular genome visualizer for bacteria and archaea☆105Jun 25, 2023Updated 2 years ago
- post processing of bacterial pangenome gene presence/absence matrices☆66Jan 19, 2026Updated 3 months ago
- Extract metadata from biosamples in NCBI☆17Mar 12, 2026Updated last month
- Fast k-mer based tool for multi locus sequence typing (MLST)☆46Sep 3, 2020Updated 5 years ago
- Targeted Detection and Reconstruction of Plasmids☆22May 7, 2024Updated last year
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Code for de novo discovery of viral families in virome data☆16Jun 20, 2024Updated last year
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13May 15, 2018Updated 7 years ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆94Mar 30, 2026Updated last month
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆121May 21, 2024Updated last year
- A toolkit to validate and consolidate antimicrobial resistance gene databases☆20Apr 21, 2023Updated 3 years ago
- Creating plasmid maps inside ggplot.☆92Sep 2, 2025Updated 8 months ago
- Assembling the cause of phenotypes and genotypes from NGS data☆29Jun 11, 2020Updated 5 years ago