SEIR Template

SEIR Template

PhyDyn v1.3.6 packs a subtemplate (Phydyn SEIR) that generates xml code that replicates the Phydyn Weifang analysis (weifang-sarscov2/beast/seir.xml)

You need BEAST version 2.6 or higher in order to install Phydyn v1.3.6.

The following steps explain how to set the same parameters used in seir.xml.

Sequences

BEAST must be able to extract the dates from the sequence names. Phydyn needs every sequence name to by suffixed by '" (exog and Il in our example). I have the following format: Guangdong/20SF201/2020_2020.06010928962_exog

• Import the sequence file with File->Import_Alignment option from the main menu.
• Click on the Tip_Dates tab

Substitution and Clack model and select the Use_tip_dates checkbox.

Starting tree

Priors

The PhyDyn tree prior: STreeLikelihoodODE