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neherlab / treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
MIT License
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Different output trees #265

Closed MarliesJFrancine closed 7 months ago

MarliesJFrancine commented 8 months ago

Hi!

I have a single dataset, and I used it as input in (1) timetree construction, (2) ancestral sequence reconstruction, and (3) mugration analysis. My doubt is why each tree looks very different. The sequences are the same, so my understanding would be that at least the clades of the tree would be similar, but they are not. Can you share some insight on if the trees are constructed in three different ways?

rneher commented 7 months ago

The tree might be rooted differently. time tree construction reroots the tree. ancestral reconstruction and mugration should not change the tree other than removing zero length branches (if you don't provide a tree, a tree will be build using fasttree).

MarliesJFrancine commented 7 months ago

Thank you! That was indeed the difference :)