nextstrain/nextclade-3.9.1.zip
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nextstrain-nextclade-5fdc5e2
.all-contributorsrc
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.cargo
config.toml
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.dockerignore
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ISSUE_TEMPLATE
01_report_bug.md
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02_request_feature.md
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03_ask.md
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04_discuss.md
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config.yml
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dependabot.yml
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pull_request_template.md
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workflows
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builder-docker-image.yml
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cli.yml
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nextstrain-docker-base.yml
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web.yml
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.gitignore
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CHANGELOG.md
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CONTRIBUTING.md
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Cargo.lock
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Cargo.toml
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LICENSE
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Makefile
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README.md
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clippy.toml
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data
README.md
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adenovirus
hadv-a
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genemap.gff
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reference.fasta
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scripts
get-sequences.sh
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id.txt
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sequences.fasta
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ebola
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reference.fasta
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sequences.fasta
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enterovirus
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sequences.fasta
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flu
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sequences.fasta
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sequences.fasta
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pb2
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ha_reversions
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ma
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sequences.fasta
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pb2
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sequences.fasta
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vic
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sequences.fasta
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sequences.fasta
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pb2
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sars-cov-2
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genemap.gff
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reference.fasta
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sequences.fasta
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zika
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reference.fasta
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sequences.fasta
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docker
cross
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docker-dev.dockerfile
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docker-prod-alpine.dockerfile
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docker-prod-debian.dockerfile
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docker-prod-scratch.dockerfile
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docs
Dockerfile
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Makefile
876 Bytes
README.md
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_static
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css
custom.css
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favicon.ico
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_templates
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assets
nextstrain_logo.svg
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prerelease-warning.md
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release-instructions.md
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ui.gif
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changes
CHANGELOG.md
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CHANGELOG.old.md
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index.rst
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conf.py
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dev
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docs-meta.md
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index.rst
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macos.md
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old-versions.md
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environment.yml
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index.rst
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make.bat
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user
algorithm
01-sequence-alignment.md
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02-translation.md
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03-phylogenetic-placement.md
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04-clade-assignment.md
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05-mutation-calling.md
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06-quality-control.md
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07-pcr-primer-changes-detection.md
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index.rst
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nextclade-pango.md
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assets
algo_private-muts-classification.png
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algo_private-muts.png
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web_QC.png
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web_alignment-tip.png
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web_alignment.png
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web_autosuggest-result.png
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web_click-gene.png
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web_export.png
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web_load-sequences.png
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web_mut-tooltip.png
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web_overview.png
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web_select-dataset.png
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web_tree-builder.png
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web_tree.png
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web_trigger-suggest.png
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datasets.md
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faq.md
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input-files
01-sequence-data.md
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02-reference-sequence.md
1.0 kB
03-genome-annotation.md
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04-reference-tree.md
10.0 kB
05-pathogen-config.md
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compression.md
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index.rst
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links.md
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migration-v3.md
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nextclade-cli
index.rst
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installation
build-from-source.md
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conda.md
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docker.md
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index.rst
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standalone.md
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reference.md
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usage.md
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nextclade-web
analysis-results-table.md
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export.md
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getting-started.md
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index.rst
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performance-tips.md
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phylogenetic-tree-view.md
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url-parameters.md
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output-files
01-all.md
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02-nuc-alignment.md
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03-translations.md
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04-results-tsv.md
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05-results-json.md
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06-tree.md
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compression.md
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errors-and-warnings.md
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index.rst
751 Bytes
terminology.md
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packages
nextclade-cli
Cargo.toml
1.6 kB
src
bin
nextclade.rs
253 Bytes
cli
mod.rs
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nextclade_cli.rs
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nextclade_dataset_get.rs
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nextclade_dataset_list.rs
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nextclade_loop.rs
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nextclade_ordered_writer.rs
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nextclade_read_annotation.rs
1.5 kB
nextclade_seq_sort.rs
12.0 kB
print_help_markdown.rs
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verbosity.rs
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dataset
dataset_download.rs
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dataset_table.rs
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mod.rs
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io
http_client.rs
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mod.rs
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lib.rs
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nextclade-web
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.eslintignore
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config
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next
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addWebpackPlugin.ts
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getEnvVars.ts
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loaders
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withWebpackWatchPoll.ts
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withoutDebugPackage.ts
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withoutMinification.ts
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nodemon
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cli.dev.json
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cli.prod.json
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dev.json
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eslint.fix.json
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eslint.json
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lint.json
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profile.json
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serve.json
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stylelint.fix.json
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stylelint.json
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infra
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lib
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EnvVarError.js
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clear.js
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findModuleRoot.js
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getenv.js
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manifest.json
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src
assets
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components
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LogoGisaid.tsx
703 Bytes
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Error
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error-types
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ErrorNetworkConnectionFailure.tsx
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ErrorNetworkRequestFailure.tsx
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NextcladeV2ErrorContent.tsx
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Export
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ExportTabColumnConfig.tsx
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ExportTabMain.tsx
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FilePicker
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TextInputMonospace.tsx
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UploadedFileLoadingInfo.tsx
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useUploadZone.ts
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GeneMap
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GeneMapAxis.tsx
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GeneMapTable.tsx
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getAxisLength.ts
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Help
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SelectGeneHelp.tsx
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SelectRefNodeHelp.tsx
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Layout
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Layout.tsx
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NavigationLink.tsx
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Loading
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Main
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1.4 kB
DatasetCurrent.tsx
2.5 kB
DatasetCurrentSummary.tsx
2.6 kB
DatasetCurrentUpdateNotification.tsx
2.0 kB
DatasetCustomizationIndicator.tsx
2.7 kB
DatasetInfo.tsx
7.7 kB
DatasetListEntry.tsx
627 Bytes
DatasetPage.tsx
488 Bytes
DatasetSelector.tsx
3.6 kB
DatasetSelectorList.tsx
4.6 kB
Downloads.tsx
5.3 kB
ExampleSequencePicker.tsx
3.5 kB
MainInputForm.tsx
6.0 kB
MainPage.tsx
452 Bytes
MainSectionTitle.tsx
515 Bytes
QuerySequenceFilePicker.tsx
2.1 kB
QuerySequenceList.tsx
4.4 kB
RunPanel.tsx
4.5 kB
StepDatasetSelection.tsx
2.4 kB
SuggestionAlertDatasetPage.tsx
2.1 kB
SuggestionAlertMainPage.tsx
4.7 kB
SuggestionPanel.tsx
4.5 kB
Title.tsx
2.1 kB
Results
ButtonFilter.tsx
1.1 kB
ButtonHelp.tsx
2.2 kB
Circle.tsx
1.2 kB
ColumnAaMotifs.tsx
10.5 kB
ColumnClade.tsx
1.1 kB
ColumnCoverage.tsx
622 Bytes
ColumnCustomNodeAttr.tsx
1.1 kB
ColumnFrameShifts.tsx
1.3 kB
ColumnGaps.tsx
1.9 kB
ColumnInsertions.tsx
1.9 kB
ColumnMissing.tsx
4.1 kB
ColumnMutations.tsx
4.2 kB
ColumnName.tsx
2.3 kB
ColumnNameTooltip.tsx
4.9 kB
ColumnNonACGTNs.tsx
1.0 kB
ColumnQCStatus.tsx
1.7 kB
ColumnStopCodons.tsx
1.3 kB
HelpTips
HelpTipsColumnClade.mdx
230 Bytes
HelpTipsColumnCoverage.mdx
59 Bytes
HelpTipsColumnFrameShifts.mdx
509 Bytes
HelpTipsColumnGaps.mdx
268 Bytes
HelpTipsColumnId.mdx
222 Bytes
HelpTipsColumnInsertions.mdx
308 Bytes
HelpTipsColumnMissing.mdx
272 Bytes
HelpTipsColumnMut.mdx
341 Bytes
HelpTipsColumnNonAcgtn.mdx
293 Bytes
HelpTipsColumnQC.mdx
111 Bytes
HelpTipsColumnRowIndex.mdx
343 Bytes
HelpTipsColumnSeqName.mdx
178 Bytes
HelpTipsColumnSeqViewGeneLegend.tsx
1.5 kB
HelpTipsColumnSeqViewNucLegend.tsx
1.2 kB
HelpTipsColumnStopCodons.mdx
596 Bytes
HelpTipsGeneMap.mdx
632 Bytes
ListOfFrameShifts.tsx
1.1 kB
ListOfGaps.tsx
867 Bytes
ListOfInsertions.tsx
6.0 kB
ListOfMutationsGeneric.tsx
1.6 kB
ListOfMutationsLabeled.tsx
2.2 kB
ListOfNonACGTNs.tsx
1.1 kB
ListOfNucMuts.tsx
3.2 kB
ListOfQcIsuues.tsx
3.2 kB
ListOfStopCodons.tsx
1.1 kB
RefNodeSelector.tsx
5.0 kB
ResultsControlsSort.tsx
1.1 kB
ResultsFilter.tsx
8.2 kB
ResultsPage.tsx
1.6 kB
ResultsStatus.tsx
6.2 kB
ResultsTable.tsx
19.8 kB
ResultsTableRow.tsx
2.3 kB
ResultsTableRowError.tsx
1.1 kB
ResultsTableRowPending.tsx
1.3 kB
ResultsTableRowResult.tsx
7.2 kB
ResultsTableStyle.tsx
3.2 kB
Tooltip.tsx
1.2 kB
getStatusIconAndText.ts
1.6 kB
splitToRows.ts
461 Bytes
truncateList.tsx
271 Bytes
SequenceView
ListOfAaChangesFlatTruncated.tsx
2.0 kB
ListOfAaSubs.tsx
2.3 kB
ListOfAminoacidDeletions.tsx
2.0 kB
ListOfPcrPrimerChanges.tsx
1.3 kB
ListOfPcrPrimersChanged.tsx
668 Bytes
PeptideContext.tsx
7.7 kB
PeptideMarkerFrameShift.tsx
3.8 kB
PeptideMarkerInsertion.tsx
2.0 kB
PeptideMarkerMutationGroup.tsx
6.6 kB
PeptideMarkerUnknown.tsx
2.4 kB
PeptideView.tsx
3.7 kB
PeptideViewAbsolute.tsx
3.1 kB
PeptideViewRelative.tsx
3.6 kB
SequenceMarkerAmbiguous.tsx
3.6 kB
SequenceMarkerFrameShift.tsx
5.1 kB
SequenceMarkerGap.tsx
3.2 kB
SequenceMarkerInsertion.tsx
2.4 kB
SequenceMarkerMissing.tsx
2.4 kB
SequenceMarkerMutation.tsx
3.2 kB
SequenceMarkerUnsequenced.tsx
4.5 kB
SequenceSelector.tsx
8.2 kB
SequenceView.tsx
1.3 kB
SequenceViewAbsolute.tsx
4.5 kB
SequenceViewColumnHeader.tsx
2.2 kB
SequenceViewRelative.tsx
4.6 kB
SequenceViewStyles.tsx
294 Bytes
sortByCdsName.ts
534 Bytes
Settings
SeqViewSettings.tsx
6.8 kB
SettingsPage.tsx
2.4 kB
SystemSettings.tsx
5.9 kB
Tree
Form.tsx
790 Bytes
LogoPoweredByAuspice.tsx
1.7 kB
Sidebar.tsx
2.5 kB
Tree.tsx
1.5 kB
TreeIcon.tsx
309 Bytes
TreePage.tsx
484 Bytes
TreePageContent.tsx
3.4 kB
constants.ts
3.8 kB
filtering
filterByAminoacidChanges.ts
1.6 kB
filterByClades.ts
465 Bytes
filterByNucleotideMutations.ts
1.2 kB
filterByQCIssues.ts
877 Bytes
filterBySeqName.ts
377 Bytes
runFilters.ts
1.2 kB
splitFilterString.ts
195 Bytes
helpers
ErrorFatal.ts
105 Bytes
ErrorInternal.ts
239 Bytes
TFunctionInterface.ts
90 Bytes
__tests__
mergeByWith.test.ts
1.6 kB
parseAminoacidChange.test.ts
3.2 kB
parseMutation.test.ts
3.1 kB
appendDash.ts
65 Bytes
colorHash.ts
5.4 kB
errorPrototypeTojson.ts
642 Bytes
filterProps.ts
158 Bytes
formatCompatibility.ts
250 Bytes
formatDate.ts
570 Bytes
formatFrameShift.ts
212 Bytes
formatMutation.ts
1.4 kB
formatNonAcgtn.ts
224 Bytes
formatPrimer.ts
312 Bytes
formatQCFrameShifts.ts
1.5 kB
formatQCMissingData.ts
829 Bytes
formatQCMixedSites.ts
820 Bytes
formatQCPrivateMutations.ts
1.2 kB
formatQCSNPClusters.ts
857 Bytes
formatQCStopCodons.ts
702 Bytes
formatRange.ts
1.2 kB
functionPrototypeTojson.ts
478 Bytes
getAminoacidColor.ts
822 Bytes
getCopyrightYearRange.ts
288 Bytes
getHttpStatusText.ts
1.2 kB
getNucleotideColor.ts
545 Bytes
getNumThreads.ts
2.9 kB
getSafeId.ts
668 Bytes
getTextColor.ts
290 Bytes
getVersionString.ts
707 Bytes
jestUtils.ts
99 Bytes
mergeByWith.ts
1.0 kB
notUndefined.ts
264 Bytes
number.ts
323 Bytes
parseAminoacidChange.ts
1.2 kB
parseMutation.ts
955 Bytes
parsePosition.ts
292 Bytes
parseUrl.ts
2.0 kB
readFile.ts
2.7 kB
relativeMuts.ts
3.9 kB
removeUndefined.ts
230 Bytes
safeZip.ts
845 Bytes
sanitizeError.ts
513 Bytes
sanitizeRootSeq.ts
103 Bytes
saveFile.ts
1.1 kB
search.ts
919 Bytes
setOperations.ts
107 Bytes
sortResults.ts
6.7 kB
string.ts
1.3 kB
takeFirstMaybe.ts
751 Bytes
types.ts
924 Bytes
uniqueId.ts
90 Bytes
unreachable.ts
188 Bytes
useAxiosQuery.ts
1.8 kB
useTranslationSafe.ts
399 Bytes
uuid.ts
158 Bytes
hooks
useExportResults.ts
10.2 kB
useRecoilStateDeferred.ts
825 Bytes
useReloadPage.ts
336 Bytes
useResetSuggestions.ts
537 Bytes
useRunAnalysis.ts
8.6 kB
useRunSeqAutodetect.ts
6.7 kB
useStopPropagation.ts
177 Bytes
useToggle.ts
858 Bytes
i18n
detectLocale.ts
1.1 kB
i18n.auspice.ts
3.2 kB
i18n.ts
14.0 kB
resources
af
common.json
49.1 kB
am
common.json
60.8 kB
ar
common.json
61.3 kB
az
common.json
53.4 kB
bg
common.json
70.1 kB
bn
common.json
82.2 kB
bs
common.json
49.4 kB
ca
common.json
52.0 kB
cs
common.json
50.1 kB
cy
common.json
49.4 kB
da
common.json
48.5 kB
de
common.json
52.1 kB
el
common.json
72.8 kB
en
common.json
47.5 kB
es
common.json
53.0 kB
et
common.json
48.7 kB
fa
common.json
62.3 kB
fi
common.json
49.6 kB
fr
common.json
54.3 kB
ga
common.json
51.8 kB
gu
common.json
79.4 kB
ha
common.json
49.4 kB
he
common.json
55.7 kB
hi
common.json
81.8 kB
hr
common.json
49.4 kB
ht
common.json
47.3 kB
hu
common.json
52.4 kB
hy
common.json
71.2 kB
id
common.json
49.2 kB
is
common.json
49.8 kB
it
common.json
51.7 kB
ja
common.json
57.4 kB
ka
common.json
83.5 kB
kk
common.json
69.2 kB
kn
common.json
87.9 kB
ko
common.json
52.7 kB
lt
common.json
50.9 kB
lv
common.json
50.3 kB
mk