## 3.21.1 ### Fix: allow numeric keys in Auspice coloring scale Auspice JSON v2 allows both string and numeric values as the first element of coloring scale entries. Nextclade previously only accepted strings, causing deserialization failures when loading Auspice JSONs with continuous colorings (e.g. `nextstrain.org/rsv/a/genome/6y`). Numeric scale keys are now accepted. See [nextstrain/rsv#129](https://github.com/nextstrain/rsv/issues/129), [#1764](https://github.com/nextstrain/nextclade/pull/1764) by @victorlin. <table> <tbody> <tr> <td> ### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data) </td> </tr> </tbody> </table>

## 3.16.0 ### Introduce JSON Schema definitions We now provide [JSON Schema](https://json-schema.org/) definitions for some of the JSON-based Nextclade file formats. You can find the latest definitions and documentation [here](https://github.com/nextstrain/nextclade/tree/release/packages/nextclade-schemas). You can also generate schemas for your current version of Nextclade CLI using the newly added `nextclade schema write` command. These schemas enable validation and parser code generation (among other things) to help in development and maintenance of projects using JSON-based Nextclade formats. We would like to emphasize that currently all JSON-based Nextclade formats are unstable and can change even in minor and patch releases. Addition of schemas don't change these stability guarantees, but could help in reducing and fixing breakage after breaking changes. ### Implement amino acid mutation labels We added functionality to detect labeled amino acid mutations if dataset authors choose to define labels for them. This is similar to the existing labeled nucleotide mutations functionality, but for amino acid sequences. This could be useful to mark particular mutations of interest. Once datasets start adopting this functionality (by adding configuration to the `mutLabels.aaMutLabelMap` in `pathogen.json` of a dataset), you can find the results in the `privateAaMutations.labeledSubstitutions` column/field of Nextclade output files. <table> <tbody> <tr> <td> ### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data) </td> </tr> </tbody> </table>

## 3.15.3 ### fix: ensure GFF3 fields are correctly percent-encoded and decoded [GFF3 specification](https://github.com/The-Sequence-Ontology/Specifications/blob/fe73505276dd324bf6a55773f3413fe2bed47af4/gff3.md#description-of-the-format) requires certain characters in values and in attributes to be encoded using percent-encoding. Nextclade previously did not comply with this requirement, which could lead to incorrectly formatted annotation-related outputs (such as `annotation` field in JSON output or values in GFF3 output annotation). This has been fixed. <table> <tbody> <tr> <td> ### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data) </td> </tr> </tbody> </table>

## 3.15.2 ### fix: calculate phenotypes even if there's no tree Nextclade now calculates and displays phenotype data even for datasets which have no reference tree. The clade ignoring feature does not apply for such datasets (because no clade assignment is possible without a tree). ### fix: collapse -0.0 to 0.0 in phenotype values Nextclade will no longer display or output negative zeroes in phenotype data. ### fix: ensure CSV column and category selection is additive Nextclade now correctly adds all entries together, when mixing individual columns and column categories in CSV and TSV output columns selection configuration (e.g. in `--output-columns-selection` CLI argument). Previously one would incorrectly overwrite the other. ### fix: ensure canonical order of CSV columns Order of columns in CSV and TSV is now always enforced to be the same, regardless of presence or absence of certain columns. <table> <tbody> <tr> <td> ### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data) </td> </tr> </tbody> </table>

## 3.15.0 <table> <tbody> <tr> <td> ### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data) </td> </tr> </tbody> </table>

## 3.14.4 ### Fix seed coverage calculation for short references During alignment, seed coverage is now computed as the total seed length divided by the shorter of the query or reference. This ensures correct behavior when references are shorter than queries, without requiring artificially low `min_seed_cover` values. ### Nextclade Web: fix crash when using `?multi-dataset` URL parameter When used `?multi-dataset` URL parameter, Nextclade Web could crash under certain conditions. This has been fixed. ### Nextclade Web: workaround double run When using URL parameters, Nextclade could sometimes spawn multiple copies of the analysis run. This could result in duplicated sequences being reported in the results table erroneously as well as in other unwanted effects. We added a workaround to mitigate this problem. Please report bugs by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues). <table> <tbody> <tr> <td> ### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data) </td> </tr> </tbody> </table>

## 3.14.3 ### Fix dataset suggestions and sorting for short references Update minimizer-based scoring to better handle cases where the reference sequence is much shorter than the query sequence. The previous approach assumed full-genome references and could underestimate scores for partial references such as single genes. The revised method adjusts the normalization to avoid penalizing such cases, improving robustness without requiring changes to the index format. This resolves issues observed in datasets like yellow fever. This improves dataset suggestions in Nextclade Web and dataset detection in `nextclade sort` CLI command. This also changes the scale of values of column `score` in the TSV output of `nextclade sort` command. <table> <tbody> <tr> <td> ### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data) </td> </tr> </tbody> </table>

## 3.14.2 ### Nextclade Web: crash with custom Auspice JSON dataset When an Auspice JSON dataset is provided as whole-dataset input through `?dataset-json-url`, Nextclade Web could crash under certain conditions. This has been fixed. <table> <tbody> <tr> <td> ### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data) </td> </tr> </tbody> </table>