Hi everyone,
I‘m running codeml program to determine the positive selection of genes. I have 3 problems.
First, I found some cases that gene clusters are positively selected based on LRT test of M1a vs M2a and M7 vs M8. However, the M0 output indicates omega less than 1 (even very low in some cases). So I wonder why it happens, and can I determine the gene clusters under positive selection in these cases?
Second, inversely in some cases, some gene clusters don't pass the LRT test, indicating no significant positive selection happens. But M0 output indicates omega more than one. So how can I interpret this result? Also, how can I confidently judge the purifying selection (just like the LRT test of positive selection)? If not, can I determine purifying selection based on omega? (Since we hope to compare the purifying selection in the microbial communities)
Third, some omega values are 999 or 0.0001, the upper and lower limit of M0 output. I wonder how to treat these omega values. How about dismissing them?
I really appreciate any help you can provide.