phage

PHANOTATE: a gene caller for phages.

A listing of software, tools and databases useful for virome analysis

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

Learn and explore the world of phages, the viruses that attack bacteria. A window into the world of genetics.

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, prophage, 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.

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

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

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.

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.

Running phispy, but on the web

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

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

From protein to phage phylogeny in single line!