The ‘–clock-filter-iqd’ command removes n_iqd interquartile ranges from the root to tip with time regression. It filters out the new sequences because they are different from the previously defined sequences. The sequences I have added are also very similar, which causes many of the sequences to be on the same branch, and the nextstrain system trims these sequences as much as possible.
If I remove the ‘–clock-filter-iqd’ step, then the Nextstrain system will force these sequences into the build, but the collection date will infer these sequences in the future to spread out the phylogenetic tree.
Is there a way to keep all or most sequences in the refine step without re-rooting these sequences to future collection dates?