PHANOTATE: a tool to annotate phage genomes.

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

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

code repo for mobileOG-db

Identify phage regions in bacterial genomes for masking purposes

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.

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

This is the repository for GraphPhage, a phage analysis tool that integrates phage and ICE discrimination, phage integration site prediction, phage lifestyle prediction, and phage host prediction.

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

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

From protein to phage phylogeny in single line!

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

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

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

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

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

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