Trevor Bedford

Thanks for summarizing John. I'm torn here. It seems like the best command line interface is to either include `--clock-filter-iqd 4` or just leave out `--clock-filter-iqd` entirely. But I see...

Thanks John! Doing a simple `--group_by pango_lineage` with `--seq_per_group 1` was a very clever approach to the design problem. Here, I've just cleaned a few things up to: 1. Provide...

I'd view this issue as an aspect of the "semantic zoom" that we've discussed in Auspice, where you could collapse multiple nodes into nodes with larger radii. I do think...

Thanks for the catch here @AngieHinrichs. For seasonal flu we curate a [list of these "reference" sequences](https://github.com/nextstrain/seasonal-flu/blob/master/config/references_h3n2.txt) that are preferentially included. We've chosen these reference sequences to help keep clade...

So, I rebuilt these trial datasets: - Africa: https://nextstrain.org/staging/trial/focal-sampling/ncov/africa - Asia: https://nextstrain.org/staging/trial/focal-sampling/ncov/asia - Europe: https://nextstrain.org/staging/trial/focal-sampling/ncov/europe - North America: https://nextstrain.org/staging/trial/focal-sampling/ncov/north-america - Oceania: https://nextstrain.org/staging/trial/focal-sampling/ncov/oceania - South America: https://nextstrain.org/staging/trial/focal-sampling/ncov/south-america with a updated sampling...

Thanks @AngieHinrichs! And here is the second run with updated parameters: - Africa: https://nextstrain.org/staging/trial/focal-sampling-2/ncov/africa - Asia: https://nextstrain.org/staging/trial/focal-sampling-2/ncov/asia - Europe: https://nextstrain.org/staging/trial/focal-sampling-2/ncov/europe - North America: https://nextstrain.org/staging/trial/focal-sampling-2/ncov/north-america - Oceania: https://nextstrain.org/staging/trial/focal-sampling-2/ncov/oceania - South America:...

Cool! How did you handle issues with different names in GISAID sequences? We'd been attempting to standardize locations for while which tend to be quite messy. Just as a couple...

Leaving this open. We don't currently attempt to handle bootstrap values. I have noticed stochastic errors by IQ-TREE where some branches aren't resolved as they should be in particular daily...

I'm a fan of the proposal. I think general workflow of generating TSVs through pathogen-specific scripts and packaging these up with necessary labeling via `augur measurements export` makes sense to...

_Tom beat me to this, where I had similar response but different possible solution..._ Thanks so much for the detailed write up. This really helped with my own understanding. I...