The weighted LCA algorithm is identical to the weighted LCA algorithm used in Metascope. It operates as follows: In a first round of analysis, each reference sequence is given a weight. This is the number of reads that align to the given reference and that have the property that all the significant alignments for the read are to the same species as the reference sequence (but can also be to a strain or sub-species below the species node). In a second round of analysis, each read is placed on the node that is above 75% of the total weight of all references for which the read has a significant alignment.
The Weighted LCA algorithm will assign reads more specifically than the naive LCA algorithm. Because it performs two rounds of read and match analysis, it takes twice as long as the naive algorithm.