Interpretation of results "Gamma_family_likelihoods.txt"

[EmilianoMora]

Hi CAFE5 team,

Thank you for developing this tool! I am running some analyses I am struggling to understand if there is meaningful (biologically?) I can extract from the 'Gamma_family_likelihoods.txt' result file.

Lets say I am using four gamma categories (k=4) and the results look like this below:

#FamilyID Gamma Cat Mean Likelihood of Category Likelihood of Family Posterior Probability Significant
OG0000022 0.213631 1.38969e-93 3.43299e-41 4.04803e-53 N/S
OG0000022 0.59063 1.01484e-64 3.43299e-41 2.95614e-24 N/S
OG0000022 1.09484 3.13438e-51 3.43299e-41 9.13018e-11 N/S
OG0000022 2.1009 3.43299e-41 3.43299e-41 1 *

OG0000030 0.213631 5.45608e-140 6.3383e-65 8.60811e-76 N/S
OG0000030 0.59063 9.75198e-101 6.3383e-65 1.53858e-36 N/S
OG0000030 1.09484 3.77645e-81 6.3383e-65 5.95815e-17 N/S
OG0000030 2.1009 6.3383e-65 6.3383e-65 1 *

OG0000037 0.213631 1.93174e-78 1.40023e-37 1.37958e-41 N/S
OG0000037 0.59063 1.44059e-55 1.40023e-37 1.02882e-18 N/S
OG0000037 1.09484 2.8451e-45 1.40023e-37 2.03188e-08 N/S
OG0000037 2.1009 1.40023e-37 1.40023e-37 1 *

In all three OGs it seems like the likelihood of the Gamma category 2.1009 is significantly different from the 'Likelihood of Family'. But what does that mean?

In the Mendes et al paper (2020) it says that "CAFE 5 then uses an empirical Bayes approach to estimate the posterior probability of a family belonging to a rate category, which in turn enables down-stream analyses of ‘slow’ or ‘fast’ families." ... Is this result file related to that statement? And if so, is a higher Gamma category (e.g., 2.1009) associated with a faster evolution in this family when compared families that are significant for a lower Gamma category (e.g., 0.213631)?

Thank you in advance!

Cheers,
Emiliano