John Huddleston

@jsan4christ reported this issue recently to @rneher and myself. San is one of [many people who have experienced this issue](https://discussion.nextstrain.org/search?q=unknown%20root). Although there is a workaround of including the reference data...

Bumping this, since @danrlu and team [just ran into this issue in another annoyingly subtle manifestation](https://bedfordlab.slack.com/archives/C021ZG2P8NN/p1650038402840069) where the reference was in the `excluded_by_diagnostics.txt` file because it didn't have the expected...

@sidneymbell I was wondering about that point in @danrlu's Slack thread. I would expect the reference to get ignored during proximity calculations based on [the `--ignore-seqs` that specifies the root...

@jameshadfield has [implemented our subsampling logic as a script in ncov](https://github.com/nextstrain/ncov/pull/711), but we haven't revisited this with more testing. We originally planned to implement this as `augur subsample` (and @jameshadfield...

What inputs would a user expect when running `snakemake` with no arguments? I see this as akin to running `augur filter` with no inputs and expecting it to produce something....

Hi @imdanique and @ShawnSimp, there are many different reasons why IQ-TREE can fail to build a tree. In my experience with SARS-CoV-2 analyses, these issues tend to be caused by...

What do we think is the most biologically appropriate representation of these data in a data structure? - Encoding the potential recombinants as subtrees indicates strong evidence that the subtrees...

@rneher Does this look ok to you, too? This bit of the workflow is just complicated enough that I can imagine I'm missing something with this change...

Thank you, @joverlee521 for bumping and @victorlin for signing up to fix the merge conflict. The main reason I hadn't merged this already was that this PR does make a...

This change reminds me of [the opposite change that just happened in the seasonal-flu repo for epitope mutations](https://github.com/nextstrain/seasonal-flu/commit/46f72c3c577d1ae345d177229a5407d08a4c6898#diff-a38a6442c0b203a5f4c306dd2bed6b2be88b2323ea03656a09ea57d8f2f022c5). :) @trvrb's argument about ordinal values technically only considering rank instead of...