Merge pull request #1089: blog post: Auspice 2024 summary

static-site/content/blog/2024-12-16-auspice-2024.md

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+---
+author: "The Nextstrain team"
+date: "2024-12-16"
+title: "Notable changes in Auspice"
+sidebarTitle: "Notable changes in Auspice"
+---
+
+The Nextstrain team continues to improve the visualisation capabilities of
+Auspice, including new features, bug fixes and performance improvements. This
+year, we've released 19 versions and wanted to highlight some of the
+significant changes.
+
+<!--
+number of git tags in 2024 (generated by GitHub Copilot):
+git tag --list --format='%(creatordate:short)' | grep '^2024' | wc -l
+-->
+
+## Table of contents
+
+- [View in other platforms](#view-in-other-platforms)
+- [Performance improvements](#performance-improvements)
+- [Convey tip confidence through saturation](#convey-tip-confidence-through-saturation)
+- [Focus on selected](#focus-on-selected)
+- [Filter on all metadata](#filter-on-all-metadata)
+- [Full changelog](#full-changelog)
+
+## View in other platforms
+
+Historically, we have always been strong advocates for interoperability between
+platforms. For many years, Nextstrain.org has supported
+[fetching](https://nextstrain.org/fetch) HTTPS-addressable Auspice JSONs.
+[UShER](https://genome.ucsc.edu/cgi-bin/hgPhyloPlace) uses this feature to link
+to Auspice views for subtrees.
+
+Other platforms have developed a similar approach to access Auspice datasets,
+often using our RESTful API. When viewing datasets in Nextstrain, you can switch
+to supported platforms via the new **VIEW IN OTHER PLATFORMS** button at the
+bottom of the page:
+
+[![View in Other Platforms button](/blog/img/view-in-other-platforms.png)]()
+
+There are currently three supported platforms:
+
+- [Taxonium](https://taxonium.org) by Theo Sanderson (added in v2.53) – allows
+  phylogenetic visualization of large datasets.
+
+- [MicrobeTrace](https://microbetrace.cdc.gov) by US CDC (added in v2.53) –
+  allows network visualization of the Auspice phylogeny.
+
+- [Nextclade](https://clades.nextstrain.org/) (added in v2.54) – allows you to
+  add your own sequences (in-browser) to the current tree. This feature is
+  particularly useful to view additional sequences on top of the latest
+  Nextstrain view of circulating diversity. Certain requirements must be met for
+  this to work as expected, such as the root-sequence being defined for the
+  dataset. You may get more reliable results using the manually curated
+  reference Nextclade datasets, so please double check results against those.
+
+  [![View in Nextclade preview](/blog/img/view-in-nextclade.png)]()
+
+## Performance improvements
+
+As sequencing becomes more routine, the number of samples used in trees has also
+increased. Auspice tends to slow down for large trees (drawing performance 
+scales with the number of nodes), diverse genomes (calculating entropy scales
+with the number of observed mutations) and diverse metadata and geographic
+spread (the map complexity scales with number of color-by categories and number
+of locations).
+
+We've made [small
+steps](https://github.com/nextstrain/auspice/releases/tag/v2.60.0) towards
+improving performance in Auspice. Specifically, [entropy calculations are now
+skipped](https://github.com/nextstrain/auspice/pull/1879) when the panel is
+off-screen or not rendered, and [animations are now disabled for operations on
+trees with over 4,000 tips](https://github.com/nextstrain/auspice/pull/1880).
+These changes should result in a more responsive feel, especially on large
+datasets.
+
+## Convey tip confidence through saturation
+
+We've long used desaturation to convey (lack of) confidence in inferred metadata
+for branches, and we now do the same for tips. Tips with high confidence will
+still appear the same as in previous versions of Auspice. We are actively using
+this in the [H5N1
+cattle-outbreak](http://nextstrain.org/avian-flu/h5n1-cattle-outbreak/genome@2024-11-15?c=division)
+dataset where many tips lack geographic metadata:
+
+[![Confidence through saturation](/blog/img/confidence-through-saturation.png)]()
+
+## Focus on selected
+
+When viewing large phylogenetic trees with a sparse filter, it can be difficult
+to really see and understand the selected tips as they occupy a minority of the
+vertical space available. Enabling **Focus on Selected** allows the selected
+tips to take up more vertical space compared to other tips. For example,
+[filtering the SARS-CoV-2 global 6m view to one of the earliest clades, 20I
+(Alpha)](https://nextstrain.org/ncov/gisaid/global/6m@2024-10-30?d=tree&f_clade_membership=20I%20%28Alpha%29&p=full):
+
+[![Focus on Selected example](/blog/img/focus-on-selected-example.png)]()
+
+You can toggle this focus on and off in the sidebar:
+
+[![Focus on Selected toggle](/blog/img/focus-on-selected-toggle.png)]()
+
+We [plan](https://github.com/nextstrain/auspice/issues/1368) to continue
+exploring better ways to understand sets of sequences in the context of the
+larger tree, initially by better use of the horizontal axis which should help
+for early clades in the tree such as 20I (Alpha).
+
+## Filter on all metadata
+
+All categorical metadata available for the tree – i.e. all data within
+`node.node_attrs` – are now available as options for **Filter Data**. Combined
+with the **Focus on Selected** toggle [described above](#focus-on-selected),
+this provides a powerful way to explore subsets of data.
+
+[![Filter on all metadata](/blog/img/filter-on-metadata.png)]()
+
+## Full changelog
+
+Please see the
+[changelog](https://github.com/nextstrain/auspice/blob/-/CHANGELOG.md) for a
+complete summary of all changes.