As we develop more Nextclade datasets, we encounter a common pattern where we want to build a divergence tree for Nextclade instead of a time tree, but we want to root the divergence tree in the augur refine step using time information.
Ideally, we could skip the custom rules/scripts described above by allowing users to root in augur refine with time information but without building a time tree. When users request --root best to root with time information and without providing the --timetree flag, augur refine prints the following error:
Warning: To root without inferring a timetree, you must specify an explicit outgroup.
I propose that we allow users to request the "best" root when they provide metadata with time information even if they don't request a time tree. Internally, I think augur refine would still need to build a time tree and use this tree to determine the best root. Then, if the user did not provide --timetree, the tree that gets exported would be the divergence tree.
Relatedly, we potentially also want to allow users to use other time-based functionality like --clock-filter-iqd even if they don't request a time tree.
Context
As we develop more Nextclade datasets, we encounter a common pattern where we want to build a divergence tree for Nextclade instead of a time tree, but we want to root the divergence tree in the
augur refinestep using time information.We don't support this pattern directly in
refinenow, so we have different workarounds. In the seasonal flu repo, we root the divergence tree by calling thetreetime clockand then we runaugur refinewith the--keep-rootflag and without the--timetreeargument.In the measles workflow, we run
augur refinewith the--timetreeargument and default behavior where TreeTime finds the best root with time information. Then, we produce a new branch lengths JSON with the time branch lengths removed before passing that file toaugur export.This improvement is related to the issue where we often need to root with a specific reference sequence and then prune the root before building a time tree.
Description
Ideally, we could skip the custom rules/scripts described above by allowing users to root in
augur refinewith time information but without building a time tree. When users request--root bestto root with time information and without providing the--timetreeflag,augur refineprints the following error:I propose that we allow users to request the "best" root when they provide metadata with time information even if they don't request a time tree. Internally, I think
augur refinewould still need to build a time tree and use this tree to determine the best root. Then, if the user did not provide--timetree, the tree that gets exported would be the divergence tree.Relatedly, we potentially also want to allow users to use other time-based functionality like
--clock-filter-iqdeven if they don't request a time tree.