PHANOTATE: a tool to annotate phage genomes.
-
Updated
Feb 29, 2024 - Python
PHANOTATE: a tool to annotate phage genomes.
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
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
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.
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).
Report, proposal, and mvp implementation of a simple tool for use in finding motifs in genome data. 🧬
Nanopore long read assembly data pipeline for phage genomes
Illumina short read assembly data pipeline for phage
Scripts to analyze the data for the paper "An outstanding bacterial membranome requires CRISPR-Cas systems to avoid the intervention of phages" and derive the figures or subfigures shown in the manuscript.
Add a description, image, and links to the phage topic page so that developers can more easily learn about it.
To associate your repository with the phage topic, visit your repo's landing page and select "manage topics."