Angie Hinrichs
Angie Hinrichs
Congrats on the new release! It's exciting to see the new mutation categories, and I'll have to explode some trees and see what happens. :) I just noticed in an...
It seems that the whole point of auspice is its beautiful interactive display, so this seems like kind of a silly question but I'll ask anyway, just in case. Is...
I have noticed a pattern, almost exclusively in RKI sequences (but also in a few sequences from the Netherlands and France), of T11524C and A11537G occurring together in many different...
When it's time to extend the protobuf format, we should add a list/array of masked sites, so that usher can perform the same masking when the protobuf is initially created...
Hi! I'm trying out nextalign on norovirus genomes (small ssRNA, ~7.5kb, but highly diverged), and most sequences are unalignable with nextalign's default settings (`Unable to align: low seed matching rate....
Hi! This might be an Auspice thing, but since I'm using the nextstrain.org/fetch/ function I'll file it here. ### Current Behavior When I view https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/whereIsOrf1AB.json and select Color by: Genotype,...
ripples-fast fails to build in the bioconda Mac environment -- despite the build host apparently being x86_64, `__builtin_ia32_pminsw128` is not defined. In bioconda/bioconda-recipes#38446 I changed the bioconda [build.sh](https://github.com/AngieHinrichs/bioconda-recipes/blob/3d212ebcca7c4aca50100e2f0966348f14189d6b/recipes/usher/build.sh#L21) to skip...
The UCSC Genome Browser code base includes a network library with an interface analogous to knetfile.c's, but with a few extra features (HTTPS, u/p authentication, sparse file caching of complete...
When running with a large number of sequences (which I realize is no longer the norm for you Rob, but some of us may need to when starting out), it's...
Hi Theo - my group has a tree of 127k M. tuberculosis genomes, 212k nodes. The M.tb genome is 4.4Mb and there are many mutations in the tree. With nucleotide...