version 2.49.0 - 2023/09/28
Tree-specific options in the sidebar are now hidden when the tree panel is not displayed. (#1698)
Fixed a bug where the radial trees would have their inner grid circles offset. (#1693)
Fixed a bug where SVG export of the entropy panel was invalid. (#1694)
Internal changes which should not result in any different behaviour while using Auspice.
version 2.48.0 - 2023/08/31
version 2.47.0 - 2023/08/21
Entropy panel now supports more complex genome architectures and has improved styling. The JSON schema has been extended to allow segmented CDSs, which allows us to represent CDSs such as those which wrap the origin (common in HepB), and those with ribosomal slippage (nCoV, EBOV). The visual representation of CDSs now better conveys overlapping CDSs, both in the lower “nav” axis where CDSs are stacked on top of each other and in the upper “main” axis where we now view the translations for each CDS individually. A number of small genotype-related bugs have also been fixed and the internal representation of the genome streamlined. For full details please see #1684, and the schema changes are detailed in augur PR #1281.
Remove support for Node.js version 14. (#1674)
Add support for Node.js version 20. (#1673)
version 2.46.1 - 2023/06/12
version 2.46.0 - 2023/05/15
Fixed a bug where narratives with multiple datasets that had measurements panels would error when switching datasets. (#1603)
There have been a number of internal changes with this release, most of which should not result in any different behavior while using Auspice.
version 2.45.2 - 2023/03/22
Fixed a bug for continuous color scales where tips with values of zero wouldn’t appear on legend-hover or in the frequencies panel. See PR #1643 for more.
Fixed a bug where downloaded TSVs may have unescaped quotes which resulted in incorrect parsing. See PR #1649 for more.
Minor documentation updates. See PR #1638 for more.
version 2.45.1 - 2023/03/14
Small improvements to Auspice documentation. (#1588)
version 2.45.0 - 2023/03/08
version 2.44.0 - 2023/03/02
version 2.43.0 - 2023/02/07
Improvements to the measurements panel including multiple thresholds, jitter of raw measurements within color-by groups, and a sticky x-axis. See PR 1631.
version 2.42.0 - 2022/12/15
You can now turn off tip labels by selecting “none” in the dropdown. See PR #1618
A bug in the measurements panel was fixed where the mean/SD may disappear. See PR #1593
There have been a number of internal changes with this release, most of which should not result in any different behavior while using Auspice.
version 2.41.0 - 2022/11/10
version 2.40.1 - 2022/11/07
Fixed a bug where downloaded Newick trees may be empty - often this happens when there is no newick representation for the tree being displayed and in these cases a warning notification is shown. See PR #1591 for more.
Fixed a bug where branch labels prevented clicking on the underlying branches. See PR #1584 for more.
version 2.40.0 - 2022/10/21
Keep the measurements panel’s color-by means in a stable order while filtering. See PR #1566 for more.
Allow setting the “show all branch labels” toggle via the URL query
?showBranchLabels=all. See PR #1575 for more.
The legend can no longer have duplicate entries (both for user provided color scales and for continuous scales), which also prevents the display bug where legend items may be overlapping when switching to a different coloring. See issues #1521 and #1547, and PR 1576.
Re-enable temporal confidence bars for trees which include this data. See PR #1577 for more.
version 2.39.0 - 2022/10/06
A range of improvements to the measurements panel including reference sera coloring and more informative tooltips. See PR 1557 for more.
Color-by genotype dropdown: nuc (nucleotide) is now the first item in the list. See PR 1550 for more.
Fixed a bug where zooming out one level would instead jump multiple levels. See PR 1552 for more.
Added a toggle to force the display of all branch labels, rather than only those meeting a certain threshold. See PR 1554 for more.
Install documentation updated. See PR 1551 for more.
version 2.38.0 - 2022/09/16
Mutations now separate out “undeletions” & add information on what the categories represent. See PR 1542 for more.
Bugfix where certain GISAID accessions may cause a crash when clicked. See PR 1531 for more.
Duplicate / missing node names now emit a warning to the console, not an error. See PR 1543 for more.
version 2.37.3 - 2022/06/16
version 2.37.2 - 2022/05/27
version 2.37.1 - 2022/05/11
version 2.37.0 - 2022/04/28
version 2.36.0 - 2022/03/28
Dynamically update regression lines to reflect filtered data. See PR 1484 for more.
Scatterplot axes can now use “node-order” which is the order nodes appear on the rectangular tree. See PR 1494 for more.
Show an “experimental” icon and on-hover info text for the explode-tree functionality. See PR 1486 for more.
You can now use the escape key to remove a tip/branch info modal over the tree. See PR 1485 for more.
version 2.35.0 - 2022/03/16
Upgrade how we render dropdown menus, which greatly improves the display of long options (e.g. submitting labs). See PR 1482 for more.
version 2.34.1 - 2022/03/08
(Minor change) expose functions for use in auspice.us. See PR 1478 for more.
version 2.34.0 - 2022/03/02
Measurements panel intended for displaying titer or DMS data where a tip in the tree has multiple values associated with it. This function requires a dataset with a
_measurements.jsonsidecar file See PR 1452 for more.
version 2.33.0 - 2022/02/15
(Experimental) Explode phylogeny into subtrees and allow multiple trees to be provided in the dataset. See PR 1442 for more.
Categorise mutations to better understand sequence changes on branches and tips. See PR 1449 for more.
Add a datepicker to allow precise changes to the selected date range. See PR 1412 for more.
Allow build-time customizable fine print. See PR 1448 for more.
Remove scrollbar in panels when no scrolling is possible See PR 1439 for more.
Allow searching in the color-by dropdown. See PR 1456 for more.
There have also been internal changes related to how we run CI. These should not affect using Auspice as a library / CLI.
version 2.32.1 - 2021/11/11
Fix URL parsing to allow the string “narratives” to be in a dataset without it being interpreted as a narrative itself. See PR 1428 for more.
version 2.32.0 - 2021/10/20
Tree info boxes are now improved, and you can shift+click on a branch to see more information about that branch. See PR 1420 for more.
Filters in footer are now expandable to improve usability and discoverability of the true footer. See PR 1414 for more.
Fixed a bug with CSV (drag & drop) parsing. See PR 1401 for more.
Removed unnecessary postinstall step. See PR 1419 for more.
Improved image sizing in narratives. See PR 1408 for more.
Improved documentation around how to build auspice documentation!
version 2.31.0 - 2021/09/16
Improvements to our ability to zoom out in a tree, both by exposing the root branch and via a new icon next to “Zoom to Selected”. See PR 1392 for more.
version 2.30.0 - 2021/09/07
Narratives can now load sidecar files and second trees. This allows allowing frequency panel display, colouring by root-sequence, and tanglegrams. See PR 1305 for more.
.xlsx) files can be used as additional metadata for drag-and-drop. See PR 1386 for more.
Trees are now clipped to improve axes visibility. See PR 1383 for more.
Improved accession URL creation. See PR 1382 for more.
minor documentation improvements.
version 2.29.1 - 2021/07/16
Update TravisCI script to improve how we publish Auspice to npm. See PR 1380 for more.
version 2.29.0 - 2021/07/15
Note: this version may not install from npm. Please use v2.29.1 instead
Branch labels are no longer displayed if the branch is not in the selected view. See PR 1370 for more.
Clicking on a tip and then closing the info-box will result in that tip remaining as a inactivated filter. See PR 1372 for more.
Category filters in the sidebar can now be used to inactivate all active filters in a category, and if all are inactive then this may be used to re-activate them all. See PR 1371 for more.
On-hover tooltip widths are improved for the tree. See PR 1375 for more.
[bugfix] Colour scales can now have 37 values. See PR 1355 for more.
Updated files fetched by
npm run get-data
version 2.28.0 - 2021/07/05
Remove ability to download metadata TSV from GISAID datasets. Replace with acknowledgments TSV. See PR 1366.
Cleanup header fields when downloading metadata TSV, including switch to use name (eg
pango_lineage) instead of title (eg
PANGO lineage). See PR 1367.
Update styling of footer text. See PR 1364.
version 2.27.0 - 2021/06/05
version 2.26.0 - 2021/05/25
Non-continuous variables can now be used, which allows all colourings (including Genotype, if that’s the current colouring) to be scatterplot variables.
Jittering is applied when the spacing between axis variables is more than 50 pixels.
See PR 1346 for more.
Normalized frequency values now tend to zero in the absence of data. See PR 1325 for more.
Colour scale improvements:
Continuous colourings can provide a scale, which we interpolate between to get the colour scheme
Custom legend data can be provided, including display text and, for continuous variables, bounds to map legend entries to values in the data.
Displayed legend entires may be restricted by specifying them in the dataset JSON.
See PR 1340 for more.
Filtering via the sidebar UI now returns options which match each of the space-separated queries, rather than requiring an exact match of the query. See PR 1344 for more.
Legend text now takes the maximum available space. See PR 1328 for more.
version 2.25.1 - 2021/04/07
Bugfix for cases where certain interactions with scatterplot variables would cause auspice to crash. See PR 1332 for more.
version 2.25.0 - 2021/03/31
Scatterplots are now available as a tree layout. These allow graphs to be created between any two continuous traits (colourings), similar to the “clock” layout but with user-definable variables Branches and regression lines can be toggled on/off, and nodes which do not define valid values for both variables will be hidden. Note that the regression line is calculated with a free intercept, which differs from the clock view where we force it to pass through the root. See PR 1310 and PR 1326 for more.
Datasets may now define “data provenance” which will be rendered in the byline. See PR 1313 for more.
Names within the filtering UI now use the metadata-provided title, which is clearer. See PR 1327 for more.
Frequency rounding is improved for small values. See PR 1301 for more.
Node traits may define a URL which will result in the value being displayed as a link. See PR 1308 for more.
A bug was fixed which caused some datasets to crash auspice when metadata files were dragged on. See PR 1319 for more.
version 2.24.1 - 2021/03/19
[bugfix] Fixes a bug introduced in v2.24.0 where certain datasets wouldn’t load
version 2.24.0 - 2021/03/17
Frequencies are no longer normalized when the data is lacking. See PR 1278 for more.
Fixed a stack size bug, which mainly affected the TB dataset on certain browsers. See PR 1293 for more.
Root-to-tip mutations are now displayed in the tip-clicked info box. See PR 1280 for more.
Datasets may now define the default language. See PR 1303 for more.
Polish language added. See PR 1288 for more.
Tips in the tree should no longer be obscured behind the legend. See PR 1302 for more.
Dates BCE are now correctly displayed in the phylogeny axis. See PR 1297 for more.
version 2.23.0 - 2021/01/28
version 2.22.2 - 2021/01/14
[bugfix] Updated how we generate hashes for the transpiled, chunked client bundles. This prevents subtle bugs where bundles could have the same hash, but different contents, and thus stale (browser cached) chunks may be used in certain situations. This bug most probably arose in v2.22.0, so please update to this version if possible! See PR 1263 for more.
version 2.22.1 - 2021/01/13
Updated package-lock JSON file
version 2.22.0 - 2021/01/11
The address Auspice uses to fetch map tiles, including the API token, has been updated and will now only work for local installs of auspice. For help on how to specify your own address, which lets you specify custom map tile sets, see the Auspice docs. See PR 1261 for more.
Animation controls have moved and are now in the sidebar, underneath the date-slider. See PR 1262 for more.
The footer has been updated to streamline the Nextstrain accreditation and now displays “Powered by Nextstrain”. If you are serving your own version of auspice we ask for this accreditation to remain be maintained, in keeping with the spirit of scientific citations. Please also remember that customised version of auspice must make their source code available, as per Auspice’s licence. See PR 1260 for more.
version 2.21.0 - 2021/01/06
Tree rendering and zooming has been improved.
The Download Data functionality has been improved to export data reflecting the currently viewed subset of data. Additionally we export annotated Nexus trees which can be parsed by FigTree. See PR 1245 for more.
Tip labels are now user-selectable via a drop-down in the sidebar. See PR 1246 for more.
Legend values now dynamically update to reflect those in the current view. See PR 1250 for more.
Italian translation added. See PR 1256.
Amino acid labels are only shown on branches leading to big clades. See PR 1249 for more.
Colour scale generation has been refactored and a (rare) bug fixed where color-bys which defined a scale in the JSON could cause tips with no trait value set to have a colour rather than a shade of grey. See PR 1237.
Warnings added to documentation pages which are imported into Nextstrain’s (main) RTD project. See PR 1234.
Disabled a smoke-test which was stochastically failing on GitHub Actions (but which worked locally). See PR 1258 for more.
version 2.20.1 - 2020/11/19
Small bugfixes and performance improvements relating to to the features introduced in 2.20.0
version 2.20.0 - 2020/11/18
See PR 1200.
Add on-hover tooltips to the sidebar to better convey the functionality available. See PR 1200.
Improve how we space temporal grid lines (phylogeny & frequencies panels). See PR 1229.
Fix a bug in how we detected HTTP status codes. See PR 1226.
Auspice documentation is now switched to the Read The Docs platform, and available at https://docs.nextstrain.org/projects/auspice. Redirects have been added for the old GitHub pages site, and can be found in the redirect-documentation branch. See PR 1220.
version 2.19.0 - 2020/10/07
version 2.18.4 - 2020/09/28
version 2.18.3 - 2020/09/22
This version reverts the change to URL parsing introduced in 2.18.2 which broke Auspice on Safari (and perhaps other browsers).
version 2.18.2 - 2020/09/19
version 2.18.1 - 2020/08/07
Add between-paragraph padding for text rendering in (non-mobile) narratives.
version 2.18.0 - 2020/08/03
Parse narratives client side. See PR 1193 and PR 1172. This shifts the default client behavior to request a narrative in markdown format and parse it client-side. The server still retains the ability to parse narratives server-side and return narratives in JSON format, so there are no breaking changes.
Narratives can now contain multiple datasets. See PR 1193, PR 1176 and PR 1164. Narrative slides may now define their own unique datasets, with datasets preemptively fetched and cached to improve performance. Invalid datasets will show an error notification and fallback to the dataset defined by the frontmatter of the narrative.
(Bugfix) Zooming in the entropy panel by using shift/option + mouseWheel now appropriately updates the URL query. See PR 1188
(Bugfix) The animation occuring when zooming the phylogeny is now restored. See PR 1192
version 2.17.4 - 2020/07/21
(Bugfix) Improve parsing of narrative files where a regex on a large string (e.g. image encoded as a blob) would hang the server
version 2.17.3 - 2020/07/14
auspice viewto serve custom auspice client if one exists. See PR 1182.
version 2.17.2 - 2020/07/13
(Bugfix) Send error messages in the (HTTP) response body, not the status line. See PR 1181.
version 2.17.1 - 2020/06/25
(Bugfix) Metadata from drag-and-drop CSVs now shows up in the color-by menu. See PR 1177.
version 2.17.0 - 2020/06/19
You can now toggle whether the data in the frequencies panel is normalized. See PR 1158.
Improve the caching settings for the auspice server. See PR 1146.
The performance of Auspice is improved when transmission lines are not rendered. See PR 1153.
The “narratives” folder is now part of this repo and contains a number of test narratives. See PR 1170 for more details.
A bug was fixed where narrative slides would sometimes fail to update the tree as expected. See PR 1169.
A bug was fixed where loading a tree zoomed to a clade would prevent zooming out. See PR 1156.
A bug was fixed where numeric branch labels couldn’t be used as URL queries. See PR 1157.
The list of allowed nodejs versions was expanded. See PR 1166.
version 2.16.0 - 2020/05/29
Dynamically adjust deme circle size on the map when filtering. See PR 1135 for more.
Allow the genomic diversity data (the data behind the entropy panel) to be downloaded as a TSV. See PR 1144 for more.
When running the auspice server incomplete URLs can now be expanded by the server. See PR 1129 for more.
Temporarily disable integration tests from the GitHub CI. See PR 1148 for more.
Add a CC-BY license for the downloaded SVG (screenshots) . See PR 1140 for more.
Improvement in code which decides which footers to show. See PR 1118 for more.
Documentation improvements – see PR 1127 for more.
Fix an error in map positioning in some narrative slides. See PR 958 for more.
Rename test snapshots for Windows support. See PR 1122 for more.
Certain errors preventing the server from running are now caught & helpful messages printed. See PR 1140 for more.
version 2.15.0 - 2020/05/06
version 2.14.0 - 2020/04/24
Turkish translation. See PR 1079
version 2.13.0 - 2020/04/20
Add smoke-testing to check that certain URLs render by checking the presence of strings in the DOM. This is a big step towards a comprehensive testing suite in Auspice. See PR 1057
Add GitHub CI workflow to run tests etc automatically on PRs. See PR 1046
Add bundle size checks to the CI. See PR 1069
Allow the display of URL confidences to be set by a URL query (
?ci). This will allow narratives to render slides with the CI displayed. See PR 1046
Add the ability to export per-strain metadata of only those strains currently being displayed. See PR 1067
Improve error handling in the parsing of markdown in the footer. See PR 1058
Add a dot in the progress bar & a URL query for the end-of-narrative slide. See PR 1063
version 2.12.0 - 2020/04/08
Add a legend to the map! See PR 935
Improve the animation smoothness, especially for datasets with limited temporal range. See PR 920
Add Japanese translation See PR 1045
langURL query to allow the URL to choose the language.
Remove unnecessary lodash code from the bundles. See PR 1018
Update how the
Rootcomponent is imported. See PR 1029
Fix errors in the sizing of the map buttons. See PR 1040
Improve rendering of tree tip labels by only counting the selected (visible) tips. See PR 1043
version 2.11.4 - 2020/04/04
Temporarily remove SVG gradients in the tree due to bugs in multiple browsers. See PR 1042
version 2.11.3 - 2020/04/02
Add Portuguese translation. See PR 1017
Fig bug where some branches would not display on certain browsers. See PR 1022
Fix bug with selected dates shown when no genomes were selected. See PR 1011
--includeTimingargument when viewing help (
Add second node version to TravisCI. See PR 1023
Fix docs typo. See PR 1027
version 2.11.2 - 2020/03/30
version 2.11.1 - 2020/03/28
Add Lithuanian translation
Fig bugs in translation strings which contained
Fix syntax error in docs - See PR 1010
version 2.11.0 - 2020/03/27
You can now zoom out to the parent clade in the tree by clicking on the basal in-view branch. See PR 1001
Scroll gestures can now zoom the map. See PR 1002
Which panels are displayed by default can now be defined by the dataset JSON. See PR 1006
Mapbox attribution logo added to the map. See PR 1003
Improvements to contributing documentation. See PR 1000
version 2.10.0 - 2020/03/24
Tree branches which have an inferred state which differes between parent & child (i.e. different colours) now show a gradient across the branch. See PR 947
Hovering on a deme in the map now emphasizes the tips in the tree which make up that deme. See PR 940
Fix multiple bugs related to incorrect rendering of the map when downloading the SVG. See PR 925
Fix a bug relating to the ordering of legend items. See PR 979.
Update Spanish locale data (still in a partially complete state). See commit f9c8ad2
Fix a bug where the narrative table styling introduced in 2.9.0 were applied outside the narratives.
Fix all linting errors and warnings (potentially the first time this has happened!)
version 2.9.1 - 2020/03/23
Bugfix related to the byline for SARS-CoV-2 datasets when viewed on nextstrain.org
version 2.9.0 - 2020/03/23
Add language support for auspice! Currently we have an incomplete translation of the strings into Spanish, but we can now begin to crowd-source translations. See PR 953
Add shebang to shell scripts. See PR 962
Add styling to tables in narratives. See PR 966
Improve accessiblity of slide-dots in narratives. See PR 972
Fix typo in readme. See PR 963
Improve file modes in docs. See PR 964
Fix broken links in docs. See PR 967
Linting fixes. See PR 931
version 2.8.1 - 2020/03/20
Fix bug in dependencies which could prevent auspice from being built
version 2.8.0 - 2020/03/20
version 2.7.0 - 2020/03/15
Add axis labels to the tree. See PR 942
Fix a bug where the map would jump to an incorrect view position in narratives. See PR 950
Do not display “github.com” in the built-by byline (link is unchanged). See PR 949
Improve the REAMDE.
Allow translators to be specified in narratives & translators and authors (and their links) can be set as arrays. See PR 937
Add documentation about CSV/TSV drag-and-drop functionality
version 2.6.0 - 2020/03/09
version 2.5.7 - 2020/03/09
Allow lat-longs for locations only set on internal nodes.
version 2.5.6 - 2020/03/09
version 2.5.5 - 2020/03/04
version 2.5.4 - 2020/02/26
version 2.5.3 - 2020/02/12
version 2.5.2 - 2020/02/11
version 2.5.1 - 2020/02/07
Allow narrative markdown files to have CRLF line endings.
version 2.5.0 - 2020/02/05
Add URL query options to facilitate embedding nextstrain via an iframe. See PR 884
Sidebar state can be set via JSON & URL query.
A special URL query will disable rendering of the footer & header.
Improve tree & map zooming. See PR 886
The map will now automatically zoom upon changes in tree visibility (e.g. filters, time scrubbing, zoom-into-branch) or geographic resolution, unless the map has been interacted with.
The tree URL query for specifying which node in the tree is zoomed has been changed to
?label=<labelName>:<labelValue>, and the docs updated accordingly. The old syntax
?clade=<cladeName>will still work and automatically correct to the new syntax.
The set of branch labels to be displayed is now customisable.
Add documentation surrounding auspice view-settings
Improve text rendering in certain situations when the lato font is not available. See PR 882
version 2.4.1 - 2020/02/01
Fix two bigs in narrative UI. See PR 881
version 2.4.0 - 2020/01/31
version 2.3.7 - 2020/01/30
Fix a number of narrative bugs See PR 865
version 2.3.6 - 2020/01/30
version 2.3.5 - 2020/01/28
version 2.3.4 - 2020/01/28
widthprop passed to nav-bar extensions & update documentation. See PR 853
version 2.3.3 - 2020/01/27
version 2.3.2 - 2020/01/24
Minor styling changes to: (1) change min map zoom, (2) hide sidebar on GISAID pages and (3) show author in hover box. See PR 849
version 2.3.1 - 2020/01/24
Improvements to narrative text styling with the intention that narratives are more functional on mobile devices.
This version introduces experimental support for writing narratives where a page may define a section of markdown to be displayed in the main panel, instead of a tree or map. Documentation is forthcoming.
version 2.3.0 - 2020/01/23
version 2.2.4 - 2020/01/11
Fix bug in computing state when nodes lack
version 2.2.3 - 2020/01/06
version 2.2.2 - 2020/01/03
Remove unnecessary console log statements.
version 2.2.1 - 2020/01/03
Improve conversion functions to go between numeric & calendar dates. See PR 839
version 2.2.0 - 2019/12/16
Update datasets fetched via
npm run get-datato reflect the move to v2 (unified) JSONs.
Allow datasets to define their own footer text via a string of markdown formatted text. Harcoded footers are now only used on the nextstrain.org domain and will be removed as they are incorporated into their respective builds. See PR 834 and augur PR 423.
Copy contributing docs into a top-level CONTRIBUTING.md file. See PR 833.
Include fonts & other CSS assets in the auspice build to improve the behavior of auspice when offline. See PR 826.
UI improvement: Display build source (if defined via
JSON.meta.build_url), GitHub avatar (if build source is a GitHub repo) and maintainers as a byline under the title. See PR 821.
Performance improvement: Stream (v2) datasets between auspice server & auspice client. See PR 825.
version 2.1.0 - 2019/11/15
Added support in the narratives to navigate via arrow keys. In addition to improved UI, this allows
decktapeto convert narratives to PDFs, and a guide has been added to the auspice docs for this. See PR 824.
Added GISAID and GISRS logos to the footer for flu datasets. See PR 822.
Bugfix: Fix the broken implementation of the “serverAddress” client customisation and update the relevant documentation
Bugfix: Colorings in v2 JSONs were not being correctly ordered. They now maintain the order specified in the JSON. The ordering of v1 JSONs is still sorted, as per auspice v1 behavior. See PR 823.
Bugifx: The “download author data (TSV)” button no longer appears if no author information is defined in the dataset.
Minor auspice docs improvements.
version 2.0.3 - 2019/11/06
Bugfix: Correctly handle the
accession of strains both in the tip-clicked info box and in the strain TSV download. See PR 819.
version 2.0.2 - 2019/10/30
Bugfix: The ability to download per-strain metadata as a TSV file is now working again. See issue #816.
version 2.0.1 - 2019/10/25
Improved handling of traits associated with tips:
Added documentation around how auspice displays missing or unknown trait values
It a trait is defined as a coloring, then use the provided title in the tree info boxes
Improve logic as to whether a value is inferred (i.e. display associate confidence) or known. See this issue for more details.
Fix a bug where two trees couldn’t be colored by date.
version 2.0.0 - 2019/10/21
Please see the release notes for a full list of features and changes associated with auspice’s v2 release. Associated with the v2 release are much improved documentation at nextstrain.github.io/auspice
Here is a summary of the main changes:
Pie charts to represent discrete variables on a map
New dataset JSON format:
Strings parsed unchanged
Both metadata and tree data in a single JSON
Gene / Genome definitions are now in GFF format
Changes to how node data is stored
Continous, Categorical, Ordinal, and Boolean Color Scales
More information in tree info boxes
Display of second trees
Display better dates on the tree axis
Map “reset zoom” button zooms to include all demes
Consistent colouring of missing data in the tree
Removal of Twitter & Google Analytics
Improvements in the entropy panel
Auspice responds to server redirects for datasets
Importing (server) code from Auspice
New Auspice subcommand:
Ability to show a “build” source URL in the sidebar
auspice viewuses a custom Auspice client if present
version 1.39.1 - 2019/10/21
This release marks the final v1 release before auspice v2 is released.
Auspice v1 may still receive bug-fixes, and will be npm-tagged with “version1” so that it may be installed via
npm install --global auspice@version1.
Minor dependency version upgrades.
version 1.39.0 - 2019/09/12
Slight changes to the auspice splash page wording to remove the word “Locally”.
getDatasetAPI calls may now return code 204 (”no content”) resulting in the auspice splash page displayed without an error message.
Default styling of narrative text much improved.
version 1.38.2 - 2019/09/06
Fix footer for INRB Ebola builds.
version 1.38.1 - 2019/09/06
Update footer for INRB Ebola builds. cd
version 1.38.0 - 2019/08/29
version 1.37.5 - 2019/08/09
Allo increased zoom levels in map. [See PR 765](https://github.com/nextstrain/auspice/pull/765
version 1.37.4 - 2019/08/04
Improved layout of unrooted trees when zoomed into a clade. See PR 754
Remove link to “deprecated” nextflu.org site from flu page footer.
version 1.37.3 - 2019/07/29
Reinstate github dataset link in sidebar for community builds
version 1.37.2 - 2019/07/20
Fix bug where auspice would crash if the JSON contained an “annotation” property but not a “annotation.nuc” key. See issue #732
The Map panel title is now “Grography” when transmissions are not inferred. See issue #743
version 1.37.1 - 2019/07/13
Fig a bug where “unknown” values of a discrete scales (e.g. “?”) could be given a colour. They are now grey.
version 1.37.0 - 2019/07/09
Fix two bugs relating to narratives and the Map component. See PR 736
Improve logic behind when to display tip labels on the tree
version 1.36.6 - 2019/05/18
version 1.36.5 - 2019/04/17
Fix a bug in the initial rendering of the date slider. See PR 713
version 1.36.4 - 2019/03/16
Fix map deme border coloring.
version 1.36.3 - 2019/03/11
Various map improvements, including transmission ribbons, improved initial map bounds and improved deme circle sizing. See PR 712
Check mutation type against tree. (See PR 709)[https://github.com/nextstrain/auspice/pull/709]
version 1.36.2 - 2019/03/04
Update footer information. Don’t display “live” footers for “community” URLs.
version 1.36.1 - 2019/02/27
Update npm packages identified as security vulnerabilities
Fixes a bug (only in v1.36.0) where, for some datasets, interacting with the tree would cause the app to crash. Issue 708
auspice buildnow exits (with non-zero exit code) if there are errors during webpack bundling
version 1.36.0 - 2019/02/25
Improve app load times using code splitting. See PR 701
version 1.35.5 - 2019/02/08
Add acknowledgements to mumps page.
Preserve URL during 404. Issue #700
version 1.35.4 - 2019/01/28
Restore download modal functionality. Issue 699
version 1.35.3 - 2019/01/25
version 1.35.2 - 2019/01/16
version 1.34.4 - 2019/01/15
Update mumps footer
version 1.34.3 - 2018/12/18
Don’t display deme circle if lat/long is absent
version 1.34.2 - 2018/12/05
Update mumps footer
Modify the casing of how labels are displayed See PR 685
version 1.34.1 - 2018/11/29
Small change to make the ‘Second Tree’ option appear when virus segments are named according to “segment1”, “segment2” etcetera. See PR 684
version 1.34.0 - 2018/11/19
Community builds are now sourced from githubusercontent, which is the official source for “raw” files from GitHub. PR 682
version 1.33.0 - 2018/11/18
Gene names can now include
_, as well as code improvements to genotype encoding/decoding – PR 681
version 1.32.0 - 2018/11/02
version 1.31.0 - 2018/10/29
version 1.30.3 - 2018/09/19
version 1.30.2 - 2018/09/07
version 1.30.1 - 2018/09/05
version 1.30.0 - 2018/09/05
version 1.29.0 - 2018/08/31
The visibility of nodes on the tree now more accurately reflects the selected date range - PR 644
Info text is easier to read & the date range reflects the genomes in view - PR 639
version 1.28.0 - 2018/08/25
version 1.27.1 - 2018/08/24
Fixed broken navigation links
Entropy zooming bug fixed - PR 637
version 1.27.0 - 2018/08/20
Saved SVGs now include two trees (if displayed) - PR 630
version 1.26.0 - 2018/08/20
Entropy panel zoom changes are now reflected in URL state - PR 626
version 1.25.2 - 2018/08/17
version 1.25.1 - 2018/08/10
Small fixes to entropy zooming behaviour
Gaps are not counted in the entropy calculations & are not displayed in the info panel pop up
version 1.25.0 - 2018/08/09
New Entropy panel zooming functionality - PR 609
version 1.24.1 - 2018/08/08
Bugfix when changing between staging datasets - issue 618
version 1.24.0 - 2018/08/05
Tree grid improvements - PR 610
Allow negative (i.e. BCE) dates
Display y-dates and horizontal lines in the clock layout view
Improved spacing between grid points
SVG elements in the DOM are now in named groups which improves debugging and prevents incorrect-layering bugs. PR 612
Fixed a bug where the available datasets (dropdowns in sidebar) contained invalid values PR 614
Community sourced datasets (nextstrain.org/community/…) display a link to the github repo in the sidebar PR 615
Since v1.22.3 changing datasets preserved the URL queries (e.g.
?l=radial). A number of bugs relating to this have been fixed, where these queries were no longer valid for the new dataset. This also fixed potential issues related to loading datasets where the URL queries were invalid. PR 613
version 1.23.2 - 2018/07/30
Increase the padding when displaying two panels side by side to avoid bugs on different browsers / OSs. issue 574
version 1.23.1 - 2018/07/30
Improved the alignment of branch labels for the second tree
version 1.23.0 - 2018/07/28
The server no longer needs to be transpiled
The interaction between data sources (local / staging / live) has been changed.
The first part of the URL now defines the source, e.g. /flu is live, /local/flu is local, /staging/flu…
npm run server.js localDatano longer has the effect it used to!
Github committed JSONs are now accessible via /community/orgName/repoName (slightly experimental and subject to change)
JSONs are now delivered to the client using compression (when available)
Frequency JSONs are only fetched when the frequency panel is specified (in the meta JSON)
The server combines the tree & meta JSONs into a single “unified” JSON, in preparation for a move to v2.0 JSONs.
Manifest files / parsing have been moved from the server
Various improvements to the narratives (still experimental and the API is subject to change)
Second trees are specified by
/na/...?tt=ha. The old syntax is still supported for backwards compatibility.
version 1.22.3 - 2018/07/19
Trigger Docker Hub automated build to rebuild via Travis CI when master branch is pushed and tests are successful
Simplify counting of traits across tree
Restored the ability to run the non-dev server with local data PR 589
version 1.22.2 - 2018/07/10
Bugfix in tip attribute counting algorithm
version 1.22.1 - 2018/07/09
version 1.22.0 - 2018/07/03
version 1.21.3 - 2018/06/27
Show tree titles (e.g.
NA) when two trees are displayed
Multi-part datasets (e.g.
flu/seasonal/h3n2...) which are not in the manifest file can now be loaded; various bugs fixed for running locally without a manifest file.
Other minor bugfixes & package upgrades
version 1.21.2 - 2018/06/07
version 1.21.1 - 2018/06/04
Narratives are now sourced from the static github repo
version 1.21.0 - 2018/06/01
Untangling via a simple algorithm upon 2nd tree load
Segment names displayed above trees (if 2 trees)
Fix hover-info-box date bug – issue 572
version 1.20.3 - 2018/05/30
Narratives now accessed via
App now works without needing a manifest file (but the datasets dropdown needs it)
Initial load simplified
Sidebar doesn’t appear until the data is ready to be displayed
version 1.20.2 - 2018/05/21
Changes to the frequencies threshold
version 1.20.1 - 2018/05/21
Changes to the frequencies threshold
version 1.20.0 - 2018/05/15
Auspice is now served via the nextstrain.org server together with the static (gatsbyjs) site
Changes to the server code organisation
Static content removed
New splash page listing the (should only be accessed from local instances or 404s, live site splash is via the static site)
Improved page navigation API
Travis CI 🎉
Auspice version is displayed in the footer
Release script modified (Travis CI listens to
releaseand pushes a successful build to S3 which is fetched by the live server)
version 1.19.1 - 2018/05/09
Fixed a bug where proteins starting with a number (e.g. 2K) were assumed to be nucleotide genotypes.
version 1.19.0 - 2018/05/09
Improved sidebar styling on both mobile & desktop
Reset layout button doesn’t re-instantiate the PhyloTree object, rather it resets the branch thicknesses & sets the whole tree to be in view
Padding improvements - tip labels are now visible, and small clades render better.
Tip names now shown for up to 100 taxa
Branch thickness restored – issue 544
Tree panning has been removed (we no longer use
version 1.18.10 - 2018/05/07
Separate Nucleotide mutations from gaps / Ns in info-box - thanks @emmahodcroft PR 552
Frequencies y-axis is no longer rounded to the nearest 0.05
version 1.18.9 - 2018/05/03
update flu footer
start using travis CI
version 1.18.8 - 2018/05/02
temporary fix for map transmissionIndices errors (bug still exists, issue 547)
version 1.18.7 - 2018/05/02
Fix frequencies panel x-axis bug
Minor style changes
version 1.18.6 - 2018/04/30
update WNV footer
version 1.18.5 - 2018/04/27
update WNV footer
version 1.18.4 - 2018/04/26
Use exponential notation for the clock rate
version 1.18.3 - 2018/04/23
Updated the footer for LASV & WNV
version 1.18.2 - 2018/04/16
LBI color scale domain is [0, 0.7] Issue 541
Fix bug with antigenic advance & frequencies Issue 540
Hovering over a tree legend value of zero now correctly highlights matching tips
Undefined color traits are now grey on a discrete scale
Removed all references to
node.attr.strain(tree JSON) and
version 1.18.1 - 2018/04/15
Make date slider spacing consistent between animation and drag
version 1.18.0 - 2018/04/14
Tanglegrams enabled! (bugfixes & reinstate controls dropdown)
Status pages: nextstrain.org/status & nextstrain.org/status/staging
Narrative files are sourced from nextstrain.org repository
version 1.17.4 - 2018/04/10
Updated LASV footer
version 1.17.3 - 2018/04/04
Allowed arbitrary user manifests to be served
Changed how the tanglegram updates, so that it is now triggered straight after the trees update.
Updated the files downloaded from
Add lassa (LASV) footer acknowledgments.
version 1.17.2 - 2018/04/02
Job ad on splash page.
version 1.17.1 - 2018/03/28
Fix tree SVG bug Issue 535
version 1.17.0 - 2018/03/26
Now exposed via a “hidden” URL query. E.g.
Frequencies added to narrative
block in focus is part of the URL query, and can be reloaded via the URL
Second Tree / Tanglegram
Second tree can be loaded via a URL (e.g.
?tt=na). Sidebar dropdown currently disabled.
In this mode, trees are forced to be rectangular, and the map & frequencies are not displayed.
Tanglegram exists, but no untangling (yet)
Bugs still exist (which is why the sidebar has been disabled)
All JSONs (incl. frequencies, narrative) are loaded within a single Promise & dispatch
phylotree.change()only ever called once, and always in componentDidUpdate (fixes bugs where it fired in both CWRP and CDU)
old & deprecated code removed
version 1.16.5 - 2018/03/26
Authors filter is now an explicit setting in the JSONs PR 532
version 1.16.4 - 2018/03/22
version 1.16.3 - 2018/03/21
Flu footer updated
version 1.16.2 - 2018/03/21
Add redirect of www.nextstrain.org to nextstrain.org via express middleware PR 528
version 1.16.1 - 2018/03/16
Fix bug in the color scales where clades were coloured white after switching trees.
version 1.16.0 - 2018/03/16
Now works on Internet Explorer 11 (tested on windows 7)
Grid layout issue fixed for Firefox on linux/windows
Embedding Nextstrain in an iFrame works - see
version 1.15.1 - 2018/03/14
Fix Firefox branch / tip hover bug Issue 525
version 1.15.0 - 2018/03/12
Multiple genotypes (for the same amino acid) by typing in multiple comma separated AA/nuc positions. PR 523.
version 1.14.4 - 2018/03/05
Restore staging server toggle issue 514
version 1.14.3 - 2018/03/01
Bug fix where tip colours reverted to their initial colours after a layout change. issue 519
version 1.14.2 - 2018/02/28
Frequency y-axis is now dynamic
Frequency text box is more readable
Frequency normalisation has been removed
version 1.14.1 - 2018/02/27
Style tip stroke separately from branch stroke (
version 1.14.0 - 2018/02/27
Strain search (using awesomplete). This highlights the path to a single tip and increases the tip radius. Strain is stored in the URL query (
s=...) and can be restored via URL. Selected strain also appears in the info panel (top of screen).
Amino acid branch labels (for every tree) as well as clade labels if specified by the
clade_annotationattribute. AA labels are shown where the descendent visible tips account for more than 5% of the total visible tips (same as nextflu). Clade labels are always displayed.
Default geneotype gene is now HA1 if available (previously nucleotide).
ColorBy ordering (sidebar dropdown) is now ordered (via an array in
The JSON processing on initial load has been shifted from the reducers to a single action - fewer dispatches, fewer potential bugs, faster code.
Frequencies are initialised in a single action (previously 2).
tip-frequencies are now downloaded via
Frequency actions are not dispatched unless the frequency panel is loaded.
version 1.13.2 - 2018/02/26
Improve consistency of panel controls
unassignedin tree legend (if applicable)
version 1.13.1 - 2018/02/26
Tree button “reset layout” now at top right
version 1.13.0 - 2018/02/26
Frequencies are now displayed via a stream graph panel - see PR 497. These require the fetching of a separate
tip-frequenciesJSON, and must be specified in the
panelsarray of the meta.JSON.
“Panels To Display” toggles in the sidebar allow customisation of the display, and this is reflected in the URL.
-buttons in the tree have been replaced by a “reset tree” button. This resets the bounds to the entire tree & completely re-renders the tree (filters are maintained). Pan behaviour is unchanged.
React-PhyloTree interface is completely rewritten to use
phylotree.change()- see PR 501 for the API. The new interface is both easier to understand and quicker.
changePageQuery(used for changing narrative blocks) is now a single action
Ongoing narrative work (still disabled).
React sidebar has been removed (no UI changes).
version 1.12.0 - 2018/02/14
Vaccine strains are shown at their use date (in temporal trees), with dotted lines connecting them to their tips (representing collection date) (PR 498)
updateGeometryFadeuses counters to know when transitions are finished rather than
version 1.11.0 - 2018/02/05
Vaccine strains are now displayed if they are specified in
version 1.10.0 - 2018/02/05
Local Branching Index (LBI) coloring can be calculated in Auspice (code identical to nextflu) if specified in
color_options(meta JSON) (PR 491)
get_data.shscript updated to no longer download sequences & entropy JSONs
action logging middleware available for debugging / development
version 1.9.0 - 2018/01/30
Animations can now loop! This is selected via a toggle in the sidebar.
While animating, the URL displays information which defines the animation (bounds, looping, cumulative, speed). This allows the animation to start automatically by linking to this URL.
The code for the animation (i.e. the setInterval code) has been moved out of
Mapand into a separate
Animation is stopped & started by examining redux state, rather than with imperative controls.
The narrative machinery has been moved forward, but this functionality is still disabled and not present in production code.
The (rather expensive)
calendarToNumericcalculations have become part of
state.controlsso that components no longer have to calculate them from the string form.
version 1.8.0 - 2018/01/18
entropy calculated via tree
The entropy panel data is now computed within Auspice by examining mutations throughout the tree, and is throttled to improve speed under load.
Both entropy and number of mutations are available via a toggle similar to AA/NT
This results in
entropy.JSONno longer being fetched.
The entropy data is stored in redux state rather than the react component
The D3 code has been reorganised
Note that the entropy values are slightly different to those exported by Augur in some situations - see https://github.com/nextstrain/auspice/pull/478#issuecomment-358496901
genotype calculated via tree
This results in
sequences.JSONno longer being fetched.
Augur was updated to export
annotationswhich are needed for entropy gene display.
middleware / react router
All changes to the URL are now performed via middleware rather than side-effects within the action definition.
React router has been removed
Browser back/forward is detected via
window.addEventListener('popstate', this.onURLChanged)which also fires on initial page load.
Pages are selected via the
The number of proteins displayed while hovering over a branch has been limited to 7 (issue #484)
The presence of author data is checked before display (issue #488)
This changelog has been created and a step in the
releaseNewVersionscript added to prepend the version number upon release.
version 1.7.2 - 2018/1/4
Narrative / situational report
Functionality has been added, but is currently disabled via a flag in
This is currently rendered in a right-hand sidebar. This feature is not yet complete.
The following state has been added to the URL query:
genotype URLs (these were previously set as the URL but not parsed)
panel layout (grid/full)
A number of bugs regarding URL query state parsing (esp with genotype colorBys) have been fixed.
version 1.7.1 - 2017/10/31
Added mumps acknowledgment