Local version of the virus identification and analysis web server (tool set)
TrIdent- Transduction Identification: Automatic detection, classification and characterization of active transduction events in microbiomes.
LLM-powered classification of phage protein functions to identify strong lytic candidates against Klebsiella, using transfer learning and biological embeddings.
SaPhARI: An Adaptable Bioinformatics Tool for the Discovery of Novel Phage Satellites
Cocktail is a program for mathematical modelling of bacteriophage (phage) infection kinetics. Cocktail is a Windows 64-bit program and the source code can be developed in the directions that users see fit. This will be updated soon with a link to the scientific publication describing the program.
Detect elevations and gaps in read coverage on metagenome contigs or assembled genomes
Reproducible, one-command HMM-based homologue discovery for protein families across phage/viral databases (six-frame search, ORF validation, iterative convergence). macOS/Linux; Windows via WSL2.
End-to-end bacteriophage genome characterisation and phage-therapy screening — a one-click macOS app.
Creation of a local database for bacteriophages
Prediction of bacterial host for phage
Computational analysis of bacteriophage genomes including genome feature extraction, metadata integration, QC filtering, and large-scale statistical analysis.
A Nextflow pipeline for the detection, quality assessment, annotation, and classification of bacteriophages from metagenomically assembled contigs
Langevin dynamics simulation of bacteriophage-bacteria interaction
📑Reports and bioinformatics analyses from internship in Indonesia
Python code for implementing antiviral mass-balance in pre-harvest herbal plants.
A comprehensive pan-immunophagomic analysis of Pseudomonas aeruginosa, characterizing CRISPR-Cas arrays, prophage integrations, and innate bacterial defense repertoires across diverse clinical isolates.
Scripts used to prepare the "Self-splicing introns in genes of Bastillevirinae bacteriophages" paper
Predicting bacteria-phage interactions given phage and target bacterias sequenced genomes as well as hostrange interaction information. MSc Thesis @ DTU Healthtech
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