Hello
I am working on some WGS (about 16kb) measles cases from 2018 to 2024. I have one epidemiologically confirmed cluster that is not showing the tree topology I expected. Sample A infected B, C, and D. Sample D infected E and F. Attached is a snap shot of this particular cluster using the Augur pipeline. Sample A is not being shown as the MRCA and Samples B (1 nt different) and Sample D (2 nts different) are having their roots before sample A.
Is there a way to enforce topology of this cluster? I am very new to Nextstrain so the easiest option would be greatly appreciated.
Thanks