Global phylogenies of SARS-CoV-2 sequences

Preprints from the BDI Pathogen Dynamics team regarding digital contact tracing and other non-pharmaceutical interventions for Covid-19. More details on our website:

OpenABM-Covid19: an agent-based model for modelling the spread of SARS-CoV-2 (coronavirus) and control interventions for the Covid-19 epidemic

TreeCmp: comparison of trees in polynomial time

Phylogenetics between and within hosts at once, all along the genome.

SEER, reimplemented in python 🐍🔮

Sequences from HIV Easily Reconstructed

R package for statistical inference using partially observed Markov processes

Explore spaces of phylogenetic trees

Phylogenetic ANalyses of DiversificAtion

Incorporating uncertainty in tree space

Track the impact of research software.

Reconstruction of transmission trees using genomic data

Sequential analysis of phylogenies

C library for distance calculation between gene families and species trees, with a python module for creating a "signature" of a gene family tree.

R We There Yet?

An R htmlwidgets package of phylotree.js

A collection of htmlwidgets handy for epidemiology, etc.

R scatter plot htmlwidget based on D3.js