What is the difference between mummichog v1 and v2 in Functional Analysis module?

The mummichog version 2 takes into consideration of retention time information to perform pathway analysis. It is only be available if user’s data contains a retention time (“rt” or “r.t”) column. The inclusion of retention time will increase the confidence and robustness of the potential compound matches.

Another difference is that currency compounds are removed directly from the user’s selected pathway library, versus removed from potential compound hits during the permutations.