Selection of proper priors and starting values is crucial and can be a difficult exercise in the beginning.It is not always easy to pick a proper model of tree generation (tree prior), substitution model, molecular clock model or the prior distribution for an unknown parameter.2012) and phangorn (Schliep 2011) making it accessible to users familiar with phylogenetic data in R.The use of fossil evidence to calibrate divergence time estimation has a long history.If this is correct, the cytochrome c of all mammals should be equally different from the cytochrome c of all birds.
We present NELSI, an R package to simulate rates of evolution along phylogenetic trees.
This will help the investigator determine which estimates of parameters can be trusted and which cannot.
In this tutorial we will explore how priors are selected and how molecular clock calibration works using H3N2 influenza A data from the flu virus spreading in the USA in 2009.
The molecular clock model aims to estimate the substitution rate of the data.
It is important to understand under which circumstances to use which model and when molecular calibration works.