Hello,
I'm running analyses with a partition scheme (-q) and I noticed that in several cases the output trees have less taxa than the original alignment. I check the log and this happened when some species fail the chi2 test. The number of taxa removed is equal to the number of sequences failing the test, but the missing sequences are not necessarily the same that failed the test. I thought that IQ-TREE does not remove those sequences, so I'm confused when I missing those sequences.
The command that I used was for example:
iqtree -m TESTMERGE -s cluster9987_1rr.NT.aln-gb -nt 2 -bb 1000 -wbt -st DNA -q cluster9987_1rr.NT.aln-gb.partition
and the partition file looks like this:
DNA, codon1andcodon2 = 1-393\3, 2-393\3
DNA, codon3 = 3-393\3
Thanks,
Diego