I'm performing quartet likelihood mapping in iqtree/2.0.7:
iqtree2 -s ${InputAlignment} -nt 40 -spp ${PartitioningScheme} -m ${model} -lmap 2000 -n 0 -wql -lmclust ${clusters} -rcluster-max 2000 -rclusterf 10 -pre ${RunID}
The output indicates that:
INFO: Number of quartets is reduced to all unique quartets 540
However, on next line, the output continues:
Computing 2000 quartet likelihoods (one dot represents 100 quartets).
.. .................. . : 2000
And the output (*.lmap.quartetlh) has 2000 likelihoods calculated with some of the quartets having their likelihoods calculated twice. Is this an intentational implementation of the manual selection of the quartet number when the manually selected quartet number is higher than the number of unique quartets?