Open hungweichen0327 opened 9 months ago
Yes, if the tree file specifies (P1, P2), P3), O) then that's what the _tree.txt output is going to contain. However, do double check that this is the "correct" tree -- if the _BBAA.txt output is giving you a different orientation, it is for a reason.
The meaning of the different output files "_tree.txt", "_BBAA.txt", and "_Dmin.txt" is explained the documentation here in GitHub and more in detail in the paper.
All the best Milan
Dear @millanek and community,
I have questions about the order of population set when running Dusite Dtrios. If I have 3 populations (P1, P2, P3) and an outgroup population, the two orders in the population set below would have a different meaning when running Dsuite Dtrios. Because the first one indicates (P1, P2), P3), O) and the second one indicates (P2, P3) P1, O). Is that correct?
When I ran the
Dsuite Dtrios
, there were only 56 output results (meaning 56 combinations) when I had 8 populations with an outgroup population. But the output results would have 336 (8x7x6).Thus, should I use the
-t
option and give the tree file providing the relationship of 8 populations when runningDsuite Dtrios
? The output results will contain (P2, P3) P1, O) rather than (P1, P2), P3), O) if the tree is (P1, P2), P3), O)?Thank you for the help.