Sometimes we get contextual samples (pulled by being closely related to my own samples) that have lots and lots of mutations (all samples here with > 100 mutations here are collected in 2020 which is not biologically possible and must be due to sequencing/assembly errors).
I know Nextstrain team collects them and put them to exclude.txt and I could manually do that too, but we have too many automatically built trees for me to keep track of. I also try setting
clock_filter_iqd down to 3, which lead to this tree above, should I keep tuning
clock_filter_iqd down to a smaller number, or should I try something else?