I wrote quick convertor program to Kraken output to simulated blastTAB format, so MEGAN 5 can import it. (link)
This creates a four column (not 12 column) .blast file with the first two columns of interest correctly filled in.
This requires using the file my convertor generates with the synonym map feature.
I built a taxonomic tree this way, but Options --> Compute Taxonomic Profile option is not available.
Does anyone have insight into why this option is missing?