Linear gradient of likelihood needed for demo
In MapAIC, assume that the initial likelihoods of codon usage have a linear gradient from the start to the end of the mRNA, which starts higher and decreases to 0 at the poly-A tail. Make this initial weighting proportional to the weightings provided in other variables' submodules. Also, set any STOP codons to an automatic 0 based on the codon weights file for the kingdom or phylum etc in question.
Edited by Athamanatha Kitsune