a JavaScript DNA, RNA, and protein sequence viewer

Terminal-based plasmid map viewer, sequence editor, and cloning/mutagenesis workbench in pure Python

Software for prediction of plasmid sequences in metagenomic assemblies

Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biotoul.fr/)

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir

code repo for mobileOG-db

An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

Predict plasmids from uncorrected long read data

PLSDB pipeline to collect bacterial plasmids from NCBI

repository-based plasmid design

A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes

Finding regions of similarity between plasmids

DEPRECATED: Use Cenote-Taker 3 instead

A method for next-day high-throughput full plasmid sequencing from colonies

Automatically plan the most optimal expression vector using restriction enzymes.

A library for creating plasmid feature maps with zero external dependencies.

repository-based plasmid design

Plasmid Designer and DNA Editor

MODIFI is for detecting DNA base modifications and linking ECEs to their microbial hosts using PacBio metagenomic data. It performs modification calling, motif discovery, and host–ECE association analysis, supporting both HiFi and subread data.