Pinned Repositories
BDMM-Prime
Modified implementation of the BDMM multi-type birth-death model for BEAST 2.
bdsky
Birth Death Serial Skyline Model for BEAST2
BeastFX
GUIs for BEAST using Java FX to make things more pretty.
blotter
Website source code
SCORE
SCORE-material
SCoRe-tutorial
sRanges-material
stratigraphic-ranges
CoalRe
Beast2 implementation of the coalescent with reassortment
jugne's Repositories
jugne/SCORE
jugne/stratigraphic-ranges
jugne/SCoRe-tutorial
jugne/sRanges-material
jugne/BDMM-Prime
Modified implementation of the BDMM multi-type birth-death model for BEAST 2.
jugne/bdsky
Birth Death Serial Skyline Model for BEAST2
jugne/BeastFX
GUIs for BEAST using Java FX to make things more pretty.
jugne/blotter
Website source code
jugne/feast
Tasty additions to BEAST 2
jugne/fossilsim
R package for simulating fossil data on phylogenetic trees under mechanistic models of preservation and sampling
jugne/jugne.github.io
jugne/material
Links to materials for STA 426 Fall Semester 2017
jugne/pitchfork
Bayesian phylogenetic inference under models supporting explicit polytomies.
jugne/SCORE-material
jugne/Reassortment-Tutorial
Tutorial for the coalescent with reassortment
jugne/sampled-ancestors
This BEAST2 package provides MCMC proposals and post-processing tools for sampling trees containing sampled ancestors
jugne/SciPhy
Sequential Cas9 Insertion based Phylogenetics (SciPhy) for BEAST2
jugne/score-paper-material
Simulation and real data analysis for ScoRe paper
jugne/sRanges-transmission-material
jugne/sta426hs2017_project
jugne/Sta_426
jugne/TnT
jugne/TnT-material
This repository contains the code, needed to perform analyses and make figures presented in manuscript "Integrating Transmission Dynamics and Pathogen Evolution Through a Bayesian Approach" by U. Stolz, T.G. Vaughan and T. Stadler.