Louis's repositories
skylinetools
Utilities and distributions for (birth-death) skyline models.
bdskytools
A package containing several useful R-functions for reading and plotting the results of Birth-Death Skyline (BDSKY) runs in BEAST2.
SARS-CoV-2_Guangdong_genomic_epidemiology
Data used for analyses in "Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China" (Lu et al., Cell, 2020) https://doi.org/10.1016/j.cell.2020.04.023
SARS-CoV-2_Northern_California_genomic_surveillance
Data used for analyses in "Genomic Surveillance Reveals Multiple Introductions of SARS-CoV-2 into Northern California" (Deng et al., Science, 2020) https://doi.org/10.1126/science.abb9263
viroinf-hiddensee
Datasets for the ViroInf Hiddensee workshop
beast2_bdskysa_ebov_example
Example for BEAST v2.5 paper
BESP_paper-analyses
Bayesian Epoch Sampling Skyline plot (BESP) simulation study and empirical analyses
msasummary
Tools for extracting mutations and gaps in multiple sequence alignment and plotting the results
smoothingpriors
This package implements smoothing priors and related utilities for dealing with skyline objects in BEAST2.
Treponema_pallidum_in_early_modern_Europe
Data and scripts to reproduce the molecular clock dating analyses presented in "Ancient bacterial genomes reveal a formerly unknown diversity of Treponema pallidum strains in early modern Europe (Majander et al.)
TypeLinkedLocalClock
Beast 2 package which provides a mechanism for linking the rates of a local clock to the types in a MultiTypeTree (http://tgvaughan.github.io/MultiTypeTree) tree structure
rskylinetools
R package implementing function for gridding and plotting skylines.
BEAST2-unreleased-packages
Backup repository for unreleased BEAST2 packages
chCovidDashboard
Covid-19 Dashboard for Switzerland
ClaDS-tutorial
Tutorial on the ClaDS package for the Taming the BEAST website
NS-tutorial
Model selection using nested sampling tutorial for BEAST 2
ourcodingclub.github.io
The main repository for the Coding Club website
Pre-Columbian-Treponema-pallidum-from-Brazil
Data and scripts to reproduce the molecular clock dating analyses presented in " Redefining the treponemal history through pre-Columbian genomes from Brazil" (Majandar, Pla-Diaz et al)
regions_of_the_world
List of admin0, admin1 and admin2 regions of the world
sampled-ancestors
This BEAST2 package provides MCMC proposals and post-processing tools for sampling trees containing sampled ancestors