Tutorial 3: Analysing
Run the program called Tracer to analyze the output of BEAST.
When the main window has opened, choose Import Trace File... from the File menu and select the file that BEAST has created previously.
You can also download a existing log file if you have a problem to run the analysis.
Model 0 (M0) assumes one omega for all sites (Goldman & Yang 1994). The ratio of nonsynonymous substitution rate (dN) and synonymous substitution rate (dS) is a measure of selective pressure (ω = dN/dS). For example, if nonsynonymous mutations are deleterious, purifying selection will reduce their fixation rate and dN/dS will be less than 1, whereas if nonsynonymous mutations are advantageous they will be fixed at a higher rate than synonymous mutations, and dN/dS will be greater than 1. A dN/dS ratio equal to one is consistent with neutral evolution. (Bielawski & Yang 2005)
Load trees log to DensiTree:
More details are available from BEAST2-Dev/codonsubstmodels.