PHANOTATE: a tool to annotate phage genomes.

Phigaro is a scalable command-line tool for predicting phages and prophages

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

Identify phage regions in bacterial genomes for masking purposes

code repo for mobileOG-db

This is the complete code base used in Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, and Bas E. Dutilh (2015) Computational approaches to predict bacteriophage–host relationships. FEMS Microbiology Reviews doi: 10.1093/femsre/fuv048

Accelerate common Petri dish assays with AI.

DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report

Repository containing trained YOLOv5 object detection models used within OnePetri for Petri dish and plaque detection.

The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance

From protein to phage phylogeny in single line!

Using graph database techniques to understand the infectious relationships between bacteria and phages.

A reconfigurable machine learning pipeline for labeling ORFs/proteins in bacteriophage genomes and metagenomic data.

A toy MC model studying bacteria-phage coevolution dynamics. Code is meant to be readable instead of performant, or, well, good. Good for beginners in ABM

A powerful deep learning (DL) tool and the trained models for the phage gene and protein identification with convolutional neural network (CNN).

A toy Agent-Based Model of the coevolution dynamics between bacteria and phages, with a focus on environment structure

Code for Next Generation Phage Display Motif Denoising and Identification

Quality of life improvement scripts for working with https://phaster.ca (PHAge Search Tool Enhanced Release)

Report, proposal, and mvp implementation of a simple tool for use in finding motifs in genome data. 🧬

This repository contains the data and scripts used in Simulation Study of Viral Contiguous Sequence Identification Tools