I am not sure I completely understand how the wLCA works in megan, can you help?
My data consists of 454 reads (small subset) aligned against all full chloroplasts in the genus Salix. I then used both the nLCA and the wLCA (with default LCA settings, except changing Min scores to 0), to compare the results. What happens are that 189 reads was weighted from the genus to one species (S. suchowensis). When I inspected which reads were moved I found that it was only reads with alignments to two different species and where (S. suchowensis) was one of them.
However, when I then looked at the reads remaining in the genus I still found 4 reads which also had alignments to the two species but remained at the genus level. How can this be?
See photo examples below.,
Reads assigned to species example of the weighted reads
Reads at genus which were not moved?