Prediction of bacterial host for phage

A micro-site for teaching and learning microbiology and bacteriophage wet lab skills

Old repository comprising code for my HTHSCI 3BM6 phage modelling project.

PhageOrder is a python package designed to reorder phage genomes based on its terminase subunit.

Configurable short read de novo assembly container using SPAdes and bbmap

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

An Agent-Based Model simulating the coevolution dynamics between phages and bacteria. Was my essay in the ABM course by SFI

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!

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).

Phage to Shark

Nanopore long read assembly data pipeline for phage genomes

Illumina short read assembly data pipeline for phage

.m, .MAT, .PDF, .XLS files for "Canonical host-pathogen tradeoffs subverted by mutations with dual benefits"

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

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