phylodynamics

Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.

PhyloDeep is a python library for parameter estimation and model selection from phylogenetic trees, based on deep learning.

R package for phylodynamics

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (peer-reviewed)

The McCoy phylodynamics workflow

Nextstrain community build 'Molecular epidemiology of Chikungunya virus'

version 1.2.1

Code repository for the longitudinal and phylodynamic analysis in "The longitudinal dynamics and natural history of clonal haematopoiesis"

My PhD Thesis - Institute of Evolutionary Biology, University of Edinburgh, 2018

Docker and Apptainer setup for the BEAST 2 software

Tracking the spread of Foot-and-Mouth Disease virus in South America

Nextstrain community build 'Molecular epidemiology of Venezuelan equine encephalitis complex viruses'

Example for BEAST v2.5 paper

Experiments with the BEAST 2 software

This repository contains scripts to assist the Cameroon NPHL Bioinformatic Team in analyzing Mpox WGS data for outbreak tracking and characterization.

Genomic epidemiology of novel coronavirus (SARS-CoV-2) in Pakistan

my second year poster for the Graduate School Poster Day 2016