GreenGroup/RMG-Java — Issue #218: R_Recombination family not constructing averaged rate rules
Author: jwallen
Created: 2011-10-13 17:48:44+00:00
State: open

In trying to figure out how RMG-Java constructs its crazy average-of rate rules, I came across an unexpected issue: no average-of rate rules are being generated for R_Recombination. Stepping through the recursive function, we find that this occurs because the top-level node is identified as having a nonzero rank. (Presumably whoever coded this believed that an averaged rate rule was better than a rate rule with a rank of zero.) However, looking at the database, the top-level rate rule for R_Recombination clearly is listed with a rank of zero.

The end result is that, unlike other families, the R_Recombination family is using the top-level rate rule as given in the database (rather than as an average), and doing so much more often.