Angie Hinrichs

> Instead, we have G28881A > (some mutations) > T28881A, but there was never a mutation (or series of mutations ) that led to a T at 28881, so it's...

OK, thanks Josh! The public tree is a pruned-down version of a larger tree that incorporates GISAID sequences in addition to GenBank/COG-UK. I think some mutations are being removed from...

Hi @shay671 -- the 134 sequences in [list for usher issue.csv](https://github.com/yatisht/usher/files/8074398/list.for.usher.issue.csv) seem to correspond only to the smaller branch with A2480G, not all uploaded samples in https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_23199_c07fa0.json?c=pango_lineage_usher . The title...

Yes, there is a branch containing those 134 sequences: the smallest branch in your 3 colorings by nucleotide position, that includes A2480G. Your file [list for usher issue.csv](https://github.com/yatisht/usher/files/8074398/list.for.usher.issue.csv) contains 134...

I already add the internal node_# identifiers to the JSON for the `"name"` attribute of non-leaf nodes (probably following what I saw in the nextstrain/ncov JSON a couple years ago):...

Thanks -- so sorry about that, at >12 million sequences, the protobuf byte size has exceeded a constant that seemed safe enough when I wrote the code 2 years ago!...

It is fixed on the main site https://genome.ucsc.edu/cgi-bin/hgPhyloPlace Thanks again for reporting the error! For future reference, bugs in the web interface can also be reported to the UCSC Genome...

Yes, there was a server-side SEGV caused by a strange little corner case in my code that generates a VCF file with usher's imputed alleles for ambiguous bases in the...

Oh, that's not good! Thanks for letting us know, I'll take a look.

As a temporary workaround -- our test server doesn't have this problem: https://genome-test.gi.ucsc.edu/cgi-bin/hgPhyloPlace