What is the root frequency distribution and how to determine which to use

[tsa4a12]

In the params section it stated that
'''
--poisson, -p

Use a Poisson distribution for the root frequency distribution. If no -p flag is given, a uniform distribution will be used. A value can be specified (-p10, or --poisson=10); otherwise the distribution will be estimated from the gene families.
'''

How do I know when to use it or when not to use it?
I suppose some assumptions were made on the tree but I am not an expert in terms of details in construction of a phylogenetic tree...

Thanks,
Tom

[benfulton]

The root frequency distribution is used to determine the prior probability for the likelihood calculation. Dr. Hahn recommends not using this option any longer, however; the default value should be sufficient.