John Huddleston

Assign clades with Nextclade

3

## Description of proposed changes Implements an alternate approach to assigning clade labels to internal nodes and tips using Nextclade instead of `augur clades`. This approach works by: 1. exporting...

## Description of proposed changes Allow titer collections to request a titer model run per reference virus in each collection. The workflow aggregates the resulting model results into a single...

## Description of proposed changes Copies the Nextclade "subclade" column to a new "subclade_nextclade" field and adds this new column to the Auspice config JSON for H3N2 HA as a...

## Description of proposed changes Adds distance maps for all three subtypes to calculate the number of HA amino acid substitutions from the root of the tree and adds associated...

## Current Behavior @joverlee521 [noted that our workflow configuration includes references to sites to exclude from tree building, but the workflow doesn't use them](https://github.com/nextstrain/seasonal-flu/pull/231#discussion_r2105235241). This is a bug in the...

## Context MicrobeTrace supports [visualization of genetic relationships based on pairwise distance matrices](https://github.com/CDCgov/MicrobeTrace/wiki/Distance-Matrices) (see also [this tutorial video](https://www.youtube.com/watch?v=sH62msza3qo)). A long-standing request from the MT team has been for augur distance...

### Context Most Nextstrain phylogenetic workflows assume that the user has curated a FASTA file of sequences and a TSV file of metadata with matching records and the correct metadata...

augur clades should assign clades hierarchically and parsimonously

2

## Current Behavior The following H3N2 HA tree has a corresponding clades TSV file that defines a clade A.1.4 with an immediate child clade A.1.4.5 with a HA1:45N substitution (the...

Allow user to exclude specific strains from refine's clock filter

3

### Context When `augur refine` runs with the `--clock-filter-iqd` argument, `refine` can prune older strains in the tree that user may have force-included during subsampling. For example, [a recent seasonal-flu...

Store titer records in TiterRecord class and export in structured JSON format

2

The goals of this proposal are: * remove need for `eval` call when loading titers from JSON in augur’s process step * add support for multiple user-defined titer attributes such...