I have found that the gene tree root is not follwing the species tree in the case that the gene tree does not have a leaf in the most basal species. Here is a simple test case:
(((a:0.1, b:0.1):0.1, (c:0.1, (d:0.05,e:0.05):0.05):0.1):0.1, f:0.3):0.1;
and the GS map is:
You can also see a bigger example at this link (if I remember to not delete the file....):
I cannot reproduce this error but I know where it happens and the fix is very simple, could you please sent the tree files when that happens?
I did not get the files in my email