Angie Hinrichs

I think that's the web interface not matUtils JSON output -- I'll look into it.

Yep, I was calling a library function that returns '\0' for stop codons, oops -- I will detect that and use '*', thanks for pointing that out!

This will be fixed on our [test site](https://genome-test.gi.ucsc.edu/cgi-bin/hgPhyloPlace) pretty soon, but unfortunately this week has the worst timing for our release cycle (code cutoff every 3 weeks, then 1 week...

Ah, the reason is that I've fallen behind Nextstrain & WHO letters. Ah, nextclade as well. Thank you for pointing that out!

Sorry, the web interface uses simple code that translates each nucleotide substitution into its corresponding amino acid substitution independently. I'll add it to the list of badly needed improvements but...

Hi @rkdover - I'm afraid 4000 sequences is too many for the web interface, and causes a timeout which results in truncated output. It's safest to upload a much smaller...

There are several possible reasons: * Some sequences are permanently excluded because they had 10 or more equally parsimonious placements * Some sequences are temporarily excluded because they had more...

Do you not find it useful to have a different color for your uploaded samples? When there's one uploaded sample in a large branch, wouldn't it be hard to find...

@ktmeaton they are very ad-hoc & experimental, and the "Pre/Post" labels are determined by me looking at what mutations are present/absent at the nodes of the UCSC/UShER tree where I...

Yes @ilevade, that is a nice cluster of sequences, with several mutations that distinguish them from other recombinants with a similar breakpoint. But so many distinct recombinants were detected that...