I would like to make sure that I understand the way the tool blast2lca well.
Here are my questions:
it uses naive LCA algorithm, right?
–minScore, maxExpected, minPercentIdentity: do I understand right, that these parameters define which classifications to consider: for example, for default values, only the hits with the score >50, evalue <0.01 and pident>0% would be considered.
–topPercent - does it also concern the number of hits to be considered (i.e. if we have 10 hits, it will assign it to the best one automatically) or it is something else?
-in the output, what are the numbers following the taxon levels? I suppose it is some kind of confidence, but I’m not sure and I would like to know what it means exactly.
Thanks a lot for creating all these cool tools and thanks in advance for the answers,