John Huddleston

narratives: placement of tree name in tanglegram view prevents clicking "Explore the data yourself" button

1

**Current Behavior** When viewing a tanglegram in a narrative, the text of the right-hand tree name covers the "Explore the data yourself" button almost completely, making interactive exploration difficult/frustrating for...

**Current Behavior** Emphasizing text in the sidebar with Markdown's bold syntax (e.g., `A sentence **with emphasis** looks like this.`), produces a light grey text with normal font weight instead of...

## Context Each Nextstrain build displays an avatar in the build's byline on nextstrain.org. [This avatar is sourced from the GitHub repository associated with the build](https://github.com/nextstrain/auspice/blob/a0e9080dcd61249f24f6c822dfcf6478e4e07ac2/src/components/info/byline.js#L36-L51) in the Auspice config...

**Context** Each slide in a narrative gets its own navigation link (dot? button?) at the top of the narrative's left panel, as shown below.  When exploring a new narrative,...

Support multiple tip labels

2

Would it be possible to support multiple tip labels? For example, users who drag and drop their metadata with PII and are investigating a specific subtree may be interested in...

Scatterplot sometimes uses different x-axis grid line densities for negative and positive values

1

**Current Behavior** When switching between different scatterplot variables, the grid lines for the x-axis appear at different densities for negative and positive values. For example, in the following view of...

Add support for masking gap characters

5

### Context We occasionally pass sequences to augur ancestral (or other downstream tools) that include gap characters (`-`) that should actually be missing base characters (`N`). Since "augur ancestral --infer-ambiguous"...

Output case counts per day and deme

3

## Description Emit daily case counts per deme to support models like @marlinfiggins's [Rt frequency dynamics models](https://github.com/blab/rt-from-frequency-dynamics). These models consume real case counts from the CDC that have been processed...

Output cases per day, deme, and variant

2

## Description Building on the work in issue #22, output the number of cases per day, deme, and variant to support models like @marlinfiggins's Rt frequency dynamics models. Example output...

## Current Behavior `augur align` attempts to [read a reference sequence](https://github.com/nextstrain/augur/blob/a9572d5579681cb81126f022df79461667c761b9/augur/align.py#L237-L246) from either a GenBank or FASTA file and throws a generic error when a single reference sequence can't be...