From fe7a44a9cb55d5d78087c4f09a2aa50efca81430 Mon Sep 17 00:00:00 2001 From: Plemey Date: Sun, 30 May 2021 22:06:33 +0200 Subject: [PATCH] updating readme --- README.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index a07c24c..8e2a647 100644 --- a/README.md +++ b/README.md @@ -1 +1,8 @@ -# SARS-CoV-2_EUR_PHYLOGEOGRAPHY \ No newline at end of file +# SARS-CoV-2_EUR_PHYLOGEOGRAPHY +repo associated with a manuscript on SARS-CoV-2 phylogeographic spread in western Europe. + +The XMLs can be run using the hmc-develop branch of the BEAST codebase available at https://github.com/beast-dev/beast-mcmc. +- SC2eur_thGLM3cov.xml: requires the genome data from GISAID.org. Joint sequence and location inference using a discrete trait GLM with three time-homogeneous covariates +- SC2eur_epoch3covHomoCoeff.xml: uses empirical.trees and includes three time-inhomogeneous covariates +- SC2eur_epoch3covHierarchIncl.xml: uses empirical.trees and includes three time-inhomogeneous covariates along with time-inhomogeneous inclusion probabilities with a hierarchical graph prior +- SC2eur_epochTHREs.xml: uses empirical.trees and includes three time-inhomogeneous covariates, time-homogeneous random effects, and epoch rate scalars that are a function of the overall mobility data. \ No newline at end of file