In order to define the best LCA parameters for a taxonomic assignation I first used a control set of sequences (102 COI with corresponding known species).
These sequences have been BLASTn then a XML file generated under NCBI have been imported in MEGAN 5.4.0 or MEGAN 6.6.
I used the “nucl_gi2tax-Aug2016.bin” as taxonomic mapping file.
Using MEGAN 5.4.0 with the parameters (fig1), a perfect assignation was retrieved (in occurrence and frequency) : great !!
Using MEGAN 6.6 with what I suppose to be the same parameters (fig 2) the assignation was not accurate in particular for one clade for witch the assigned specie is not the correct one.
When I inspect the alignement of this clade I could see that the correct species have been filtered out despited it get the highest score. I suppose this because the special caracteres “?;” beside the score value (fig3).
I change some (all) parameters ( many tests performed) without success.
I wonder how to applied the same parameters in 6.6 as done in 5.4 in order to retreveid the same good results with Megan 5.4.0 I probably missed something ( does weighted % LCA still active), or if there is a bug in the latest version.
Could please help me this issue ?