Hi,
I am analyzing a small AA alignment (15 species, ~330 meta-partitions). When running IQTREE 1.6.8 (newest version currently available on our cluster), the software automatically detects the type accurately for about 2/3 of the partitions if I do not use the -st AA option (see copy&paste from log-file below). I ran the analysis both with and without the data type option and got the same topology with overlapping likelihoods and only very minute variations in branch lengths (20 runs without and 1 run with -st AA). What does IQTREE do with the partitions for which it was not able to automatically determine the datatype when not using the -st option? Is this something one should look out for more carefully? I searched through the documentation, but could not seem to find this specific case.
Best,
Jan Philip Oeyen
Subset Type Seqs Sites Infor Invar Model Name
1 15 920 385 279 LG4X EOG090X0LFT_EOG090X08KD_EOG090X0EXU_EOG090X0KP6
2 AA 15 1903 135 1616 LG+R2 EOG090X0GN3_EOG090X0064_EOG090X07IC
3 8 238 72 75 LG4M EOG090X0C5G
4 AA 15 305 141 71 LG+R3 EOG090X0EYV_EOG090X0EV6
5 AA 15 887 244 386 LG+F+R3 EOG090X0ACT_EOG090X0K4K_EOG090X03QT
6 AA 15 584 34 458 JTT+R2 EOG090X0662_EOG090X09VR_EOG090X0KYU