Trevor Bedford
Trevor Bedford
## Description of proposed changes This updates both Nextstrain GISAID and Nextstrain open profiles to include `Nextclade_pango` as a coloring and filter in addition to the existing `pango_lineage` coloring and...
Existing subsampling aimed at 1.5:1 ratio of regional focal samples vs global contextual samples. This commit tilts this subsampling to be a 3:1 ratio of regional focal samples vs global...
### Description of proposed changes This commit re-implements the "zoom to selected" function in the tree panel to emphasize visible nodes by expanding their "yValues" to take up 80% of...
**Current Behavior** With new filters behavior (implemented in #1200) clicking on a single tip in the tree adds this single tip as a "filter" and covers tree with gray info...
**Context** Quite commonly there will be branches from phylotree that are just out of frame and fall alongside the x or y axis. This obscures the axis labels and generally...
**Context** The implementation of a "Zoom to Selected" button on the tree has been really useful. I'll often filter to say clade 21A and then be able to just click...
**Current Behavior** Currently, genotype filtering behaves differently from other filter types. This can be immediately seen by comparing filtering to clade and filtering to genotype. Here is filtering to clades...
If we're rooting based an outgroup, it should be common to then remove this outgroup / root when displaying tree and doing analyses. I believe a good approach could be...
I'd suggest including this figure (or something like it) to visually explain SMC: [smc.pdf](https://github.com/trvrb/sismid/files/2224373/smc.pdf)