Is it possible to midpoint root a tree with refine without having time metadata available?
The docs for refine refer to treetime which states:
–reroot REROOT [REROOT …]
Reroot the tree using root-to-tip regression.
Valid choices are ‘min_dev’, ‘least-squares’, and ‘oldest’.
‘least-squares’ adjusts the root to minimize residuals of the root-to-tip vs sampling time regression, ‘min_dev’ minimizes variance of root-to-tip distances.
‘least-squares’ can be combined with --covariation to account for shared ancestry.
Alternatively, you can specify a node name or a list of node names to be used as outgroup or use ‘oldest’ to reroot to the oldest node. By default, TreeTime will reroot using ‘least-squares’. Use --keep-root to keep the current root.
I’m not quite sure how to interpret the options. It may also be a good idea to include this help text directly in refine help to have less indirection for users.
The reason I’m trying to midpoint root is that I just quickly want to build a tree and don’t want to bother with time metadata, just work off sequences.