🚧 minor edits

static-site/content/blog/2024-12-10-auspice-2024.md

@@ -7,104 +7,115 @@ 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 18 versions and wanted to highlight some of the significant
-changes.
+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
+
+- [Focus on Selected](#focus-on-selected)
+- [View in Other Platforms](#view-in-other-platforms)
+- [Performance improvements](#performance-improvements)
+- [Conveying confidence of tips through saturation](#conveying-confidence-of-tips-through-saturation)
+- [Filtering on all metadata](#filtering-on-all-metadata)
+- [Full changelog](#full-changelog)
 
 ## 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. 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):
+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@2024-12-10?d=tree&f_clade_membership=20I%20%28Alpha%29&p=full):
 
 [![Focus on Selected example](/blog/img/focus-on-selected-example.png)]()
 
-Enabling "Focus on Selected" allows the selected tips to take up more vertical
-space compared to other tips. You can toggle this focus on/off in the sidebar:
+You can toggle this focus on/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 above.
+for early clades in the tree such as 20I (Alpha).
 
 ## View in Other Platforms
 
-Interoperability between platforms is something we've been big proponents of
-(and are part of [PH4GE](https://pha4ge.org/) to help support this), and for
-many years there's been [the ability to view HTTPS-addressable JSONs within
-Nextstrain.org](http://nextstrain.org), for instance viewing
-[UShER](https://genome.ucsc.edu/cgi-bin/hgPhyloPlace) (sub)trees within
-Nextstrain.
+Interoperability between platforms is something we've been big proponents of,
+and are part of [PH4GE](https://pha4ge.org/) to help support this. 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 Nextstrain datasets,
-often using our RESTful API. When viewing datasets in Nextstrain you can switch
-over to other supported platforms via the new "view in other platforms" button
-at the bottom of the page:
+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) (added in v2.53), which scales very well to
-  large datasets
+- [Taxonium](https://taxonium.org) (added in v2.53) – scales well to large
+  datasets.
 
-- [MicrobeTrace](https://microbetrace.cdc.gov) (CDC) (added in v2.53)
+- [MicrobeTrace](https://microbetrace.cdc.gov) by US CDC (added in v2.53)
 
-- [Nextclade](https://clades.nextstrain.org/) (added in v2.54), which allows you
-  to add your own sequences (in-browser) to the current tree. 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.
+- [Nextclade](https://clades.nextstrain.org/) (added in v2.54) – allows you to
+  add your own sequences (in-browser) to the current tree. 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 people construct trees
-with has tended to increase as well. Performance in Auspice tends to slow down
-for big trees (drawing them 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
-metadata categories x number of locations).
-
-We've made small steps towards improving performance in Auspice recently
-([version 2.60.0](https://github.com/nextstrain/auspice/releases/tag/v2.60.0)).
-Specifically we [skip entropy
-calculations](https://github.com/nextstrain/auspice/pull/1879) when the panel is
-off-screen / not rendered, and we [don't animate tree operations for trees with
-over 4,000 tips](https://github.com/nextstrain/auspice/pull/1880). These changes
-should result in a more responsive feel, especially as the dataset size
-increases.
+As sequencing becomes more routine, the number of samples used in trees has also
+increased. Performance in Auspice tends to slow down for big trees (drawing them
+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).
 
-## Other features
+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.
 
-### Conveying confidence of tips through saturation (version 2.56)
+## Conveying confidence of tips 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 (circles) on the tree. If there is
-no (or very little) uncertainty in these nodes then the tips will appear the
-same as seen in previous versions of Auspice. For example we use this in [the
-current H5N1
+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)
-where geographic metadata is not available for many tips:
+dataset where many tips lack geographic metadata:
 
 [![Confidence through saturation](/blog/img/confidence-through-saturation.png)]()
 
-### Filtering on all metadata (v2.52.0)
+## Filtering on all metadata
 
-All non-continuous metadata defined across the tree -- i.e. all data within
-node.node_attrs -- is now available as options in the "Filter Data" sidebar.
-Combined with the "focus on selected" toggle described above this provides a
-powerful way to explore subsets of data in context.
+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/master/CHANGELOG.md) for
-a complete summary of all changes, bugfixes etc.
+[changelog](https://github.com/nextstrain/auspice/blob/-/CHANGELOG.md) for a
+complete summary of all changes.