CAVEPM 2016 Poster

On May 16 and 17th, 2016, Guelph hosted the annual conference of the Canadian Association of Veterinary and Preventative Medicine. The theme of the conference was “Thinking Outside the Epidemiological Tool Box”, and saw presentations on disease surveillance, risk profiles, modelling, and other topics. I contributed a poster to the conference on phylodynamic modelling, which I will also include here Continue reading

Genetic sequence data generation with PhyloTrees.jl

I’ve been working on a Julia package for working with phylogenetic trees for the last month or so. This package is called PhyloTrees.jl. I’ve made a small introduction to its use in an IJulia notebook, check it out here, and let me know what you think of the interface!

PhyloTrees.jl will primarily be used for the simulation of genetic sequence data from defined phylogenetic trees. Additional features including inference of phylogenetic trees, and further input/output options are planned for the near future. Check it out if you are a Julia user interested in bioinformatics!

Introduction to Pathogen.jl

Pathogen.jl is a package that provides utilities for the simulation and inference of pathogen phylodynamics, built in the Julia language. Specifically, Pathogen.jl presents an extension to the individual level infectious diesase transmission models (ILMs) of Deardon et al. (2010), to simultaneously model infectious disease transmission and evolution. Pathogen genomic sequences are used in conjunction with the covariate and disease state information of individuals to infer disease transmission pathways, external disease pressure, and infectivity parameters.

Continue reading