I did selection pressure analysis on viral genomes using MEME, SLAC and FUBAR on Datamonkey server. I am using p value < 0.05 for MEME and SLAC. Do I have to do any type of multiple test correction on the p-value given by MEME and SLAC ? How can I do Bonferroni Test if I have 85 sequences each with 1250 animo acids ?
Correcting for multiple tests is done based on the number of tests performed, not the size of the dataset. For example, if you split your viral genomes up into N coding loci alignments to test for selection, you'll need to correct assuming N tests.
One way to think about a Bonferroni correction is simply dividing the p-value threshold by the number of tests. You can also easily adjust a vector of p-values under different approaches using
p.adjust() in R.