Which P-value Does CAFE 5 Use to Determine Gene Family Significance?

[Biodb-BinLi]

The output file from CAFE 5 indicates whether a gene family is significant. However, CAFE 5 computes several p-values, namely:

• Family-wide P-value: Indicates if the overall size distribution of the gene family significantly deviates from random expectations.
• Viterbi P-values: Evaluate if changes in gene family size (expansion or contraction) on specific branches are significant.
• Cut P-value: Identifies the branch that most contributes to the family's overall significance.

Question: Which p-value does CAFE 5 specifically use to determine the significance of a gene family? Any guidance or insights would be highly appreciated!

[benfulton]

I feel like you've answered your own question here. The family-wide P-value is the value that corresponds to the entire family rather than a specific branch. Is there a particular number or symbol in the output that you're asking about?