# JBrowse 2 Documentation

> JBrowse 2 is a pluggable, open-source genome browser that runs as a web app, a desktop app, and as embeddable React components, with linear, circular, dotplot, synteny, and spreadsheet views.

Each link points to the raw Markdown for that documentation page.

## General

- [Introduction](https://jbrowse.org/jb2/docs/index.md)
- [Cookbook (config recipes)](https://jbrowse.org/jb2/docs/cookbook.md)
- [Embedded components](https://jbrowse.org/jb2/docs/embedded_components.md)
- [Embedding in R / Shiny](https://jbrowse.org/jb2/docs/jbrowser.md)
- [Embedding in Python](https://jbrowse.org/jb2/docs/jbrowse_anywidget.md)
- [Command line tools (JBrowse CLI)](https://jbrowse.org/jb2/docs/cli.md)
- [Static image export (@jbrowse/img)](https://jbrowse.org/jb2/docs/jbrowse-img.md)
- [Screenshot a live view (@jbrowse/capture)](https://jbrowse.org/jb2/docs/jbrowse-capture.md)
- [FAQ](https://jbrowse.org/jb2/docs/faq.md)
- [Troubleshooting](https://jbrowse.org/jb2/docs/troubleshooting.md)

## Getting started

- [JBrowse desktop quick start](https://jbrowse.org/jb2/docs/quickstart_desktop.md)
- [JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web.md)

## User guide

- [User guide](https://jbrowse.org/jb2/docs/user_guide.md)
- [General usage: Basic usage](https://jbrowse.org/jb2/docs/user_guides/basic_usage.md)
- [General usage: Connections](https://jbrowse.org/jb2/docs/user_guides/connections.md)
- [General usage: Editing a track's plot as text](https://jbrowse.org/jb2/docs/user_guides/edit_plot.md)
- [General usage: Export R script](https://jbrowse.org/jb2/docs/user_guides/r_export.md)
- [General usage: Highlights](https://jbrowse.org/jb2/docs/user_guides/highlights.md)
- [General usage: Installing plugins](https://jbrowse.org/jb2/docs/user_guides/plugin_store.md)
- [General usage: Opening track hubs by URL](https://jbrowse.org/jb2/docs/user_guides/hub_url.md)
- [Track types: Alignments track](https://jbrowse.org/jb2/docs/user_guides/alignments_track.md)
- [Track types: GC content track](https://jbrowse.org/jb2/docs/user_guides/gc_content_track.md)
- [Track types: Gene track](https://jbrowse.org/jb2/docs/user_guides/gene_track.md)
- [Track types: GWAS / Manhattan track](https://jbrowse.org/jb2/docs/user_guides/gwas_track.md)
- [Track types: Hi-C track](https://jbrowse.org/jb2/docs/user_guides/hic_track.md)
- [Track types: MAF track](https://jbrowse.org/jb2/docs/user_guides/maf_track.md)
- [Track types: Multi-row feature track](https://jbrowse.org/jb2/docs/user_guides/multirow_feature_track.md)
- [Track types: Multi-sample variant display](https://jbrowse.org/jb2/docs/user_guides/multivariant_track.md)
- [Track types: Quantitative track](https://jbrowse.org/jb2/docs/user_guides/quantitative_track.md)
- [Track types: Sequence track](https://jbrowse.org/jb2/docs/user_guides/sequence_track.md)
- [Track types: Variant track](https://jbrowse.org/jb2/docs/user_guides/variant_track.md)
- [Views: Circular genome view](https://jbrowse.org/jb2/docs/user_guides/circular_view.md)
- [Views: Dotplot view](https://jbrowse.org/jb2/docs/user_guides/dotplot_view.md)
- [Views: Graph genome view](https://jbrowse.org/jb2/docs/user_guides/graph_genome_view.md)
- [Views: Linear synteny view](https://jbrowse.org/jb2/docs/user_guides/linear_synteny_view.md)
- [Views: Spreadsheet view](https://jbrowse.org/jb2/docs/user_guides/spreadsheet_view.md)
- [Views: SV inspector view](https://jbrowse.org/jb2/docs/user_guides/sv_inspector_view.md)
- [Sequence tools: BLAT and in-silico PCR](https://jbrowse.org/jb2/docs/user_guides/blat.md)
- [Sequence tools: Consensus sequence](https://jbrowse.org/jb2/docs/user_guides/consensus_sequence.md)
- [Sequence tools: Feature sequence panel](https://jbrowse.org/jb2/docs/user_guides/feature_sequence.md)
- [Sequence tools: Sequence search](https://jbrowse.org/jb2/docs/user_guides/sequence_search.md)
- [Analysis: Clustering rows](https://jbrowse.org/jb2/docs/user_guides/clustering.md)
- [Analysis: SV visualization](https://jbrowse.org/jb2/docs/user_guides/sv_visualization.md)

## Tutorials

- [AI agent (two fly genomes)](https://jbrowse.org/jb2/docs/tutorials/agent_synteny.md)
- [AlphaGenome predictions](https://jbrowse.org/jb2/docs/tutorials/alphagenome.md)
- [ChromHMM chromatin states](https://jbrowse.org/jb2/docs/tutorials/chromhmm.md)
- [CNV across a population (1000 Genomes)](https://jbrowse.org/jb2/docs/tutorials/population_cnv.md)
- [CNV cohort (TCGA)](https://jbrowse.org/jb2/docs/tutorials/tcga_cohort_cnv.md)
- [Display settings](https://jbrowse.org/jb2/docs/tutorials/display_settings.md)
- [Dog10K (local ancestry)](https://jbrowse.org/jb2/docs/tutorials/local_ancestry.md)
- [Dog10K (loss-of-function allele)](https://jbrowse.org/jb2/docs/tutorials/dog10k_lof.md)
- [Dog10K (selected haplotype)](https://jbrowse.org/jb2/docs/tutorials/dog10k_selection.md)
- [Dog10K (SVs)](https://jbrowse.org/jb2/docs/tutorials/dog10k_svs.md)
- [Embedding JBrowse](https://jbrowse.org/jb2/docs/tutorials/embed_linear_genome_view.md)
- [Gene density (RefSeq, RepeatMasker)](https://jbrowse.org/jb2/docs/tutorials/gene_density.md)
- [Gene prediction review](https://jbrowse.org/jb2/docs/tutorials/gene_prediction_review.md)
- [genomes.jbrowse.org (basic usage)](https://jbrowse.org/jb2/docs/tutorials/genomes_basics.md)
- [genomes.jbrowse.org (proteins)](https://jbrowse.org/jb2/docs/tutorials/genomes_proteins.md)
- [genomes.jbrowse.org (RepeatMasker rows)](https://jbrowse.org/jb2/docs/tutorials/repeatmasker_classes.md)
- [genomes.jbrowse.org (synteny)](https://jbrowse.org/jb2/docs/tutorials/genomes_synteny.md)
- [JBrowse CLI with Desktop](https://jbrowse.org/jb2/docs/tutorials/cli_desktop.md)
- [LD across an inversion (mosquitoes)](https://jbrowse.org/jb2/docs/tutorials/ld_mosquitoes.md)
- [LD at a sweep (human)](https://jbrowse.org/jb2/docs/tutorials/ld_human.md)
- [Low-mappability regions](https://jbrowse.org/jb2/docs/tutorials/mappability_qc.md)
- [Marks over a BAM (insert size)](https://jbrowse.org/jb2/docs/tutorials/read_marks.md)
- [Marks over a BED (Alu age)](https://jbrowse.org/jb2/docs/tutorials/alu_age.md)
- [Methylation (bisulfite)](https://jbrowse.org/jb2/docs/tutorials/bisulfite.md)
- [Methylation (long-read)](https://jbrowse.org/jb2/docs/tutorials/methylation.md)
- [Mutation cohort (TCGA)](https://jbrowse.org/jb2/docs/tutorials/tcga_cohort_mutations.md)
- [Organelle map (human mitochondrion)](https://jbrowse.org/jb2/docs/tutorials/organelle_map.md)
- [Pangenome (cattle)](https://jbrowse.org/jb2/docs/tutorials/pangenome_cattle.md)
- [Pangenome (hosting your own graph)](https://jbrowse.org/jb2/docs/tutorials/pangenome_prepare_graph.md)
- [Pangenome (HPRC pt 1, graph alleles and haplotypes)](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc.md)
- [Pangenome (HPRC pt 2, haplotypes against each other)](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc_haplotypes.md)
- [Pangenome (HPRC pt 3, repeat lengths)](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc_repeats.md)
- [Pangenome (Minigraph-Cactus)](https://jbrowse.org/jb2/docs/tutorials/pangenome_cactus.md)
- [Pangenome (mouse)](https://jbrowse.org/jb2/docs/tutorials/pangenome_mouse.md)
- [Pangenome (pggb)](https://jbrowse.org/jb2/docs/tutorials/pangenome_ecoli.md)
- [Phased trio (1000 Genomes)](https://jbrowse.org/jb2/docs/tutorials/analyze_trio.md)
- [Proteins (TP53 structures)](https://jbrowse.org/jb2/docs/tutorials/tp53_structures.md)
- [Proteins (variants pt 1, sickle cell)](https://jbrowse.org/jb2/docs/tutorials/protein_variants_sickle_cell.md)
- [Proteins (variants pt 2, dog SOD1)](https://jbrowse.org/jb2/docs/tutorials/protein_variants_dog_myelopathy.md)
- [Proteins (variants pt 3, grape AGL11)](https://jbrowse.org/jb2/docs/tutorials/protein_variants_seedless_grape.md)
- [Proteins (variants pt 4, KRAS G12)](https://jbrowse.org/jb2/docs/tutorials/protein_variants_kras.md)
- [Proteins (variants pt 5, TP53 R248)](https://jbrowse.org/jb2/docs/tutorials/protein_variants_tp53.md)
- [Proteins (variants pt 6, BRAF V600)](https://jbrowse.org/jb2/docs/tutorials/protein_variants_braf.md)
- [QTL mapping (BXD)](https://jbrowse.org/jb2/docs/tutorials/bxd_qtl.md)
- [RNA-seq (differential transcript usage)](https://jbrowse.org/jb2/docs/tutorials/dtu.md)
- [RNA-seq visualization](https://jbrowse.org/jb2/docs/tutorials/rnaseq.md)
- [Selection scans (DGRP)](https://jbrowse.org/jb2/docs/tutorials/population_genomics.md)
- [Single-cell ATAC pseudobulk](https://jbrowse.org/jb2/docs/tutorials/scatac_pseudobulk.md)
- [Single-cell RNA pseudobulk](https://jbrowse.org/jb2/docs/tutorials/scrna_pseudobulk.md)
- [SV callset review](https://jbrowse.org/jb2/docs/tutorials/sv_callset_review.md)
- [SVs (1000 Genomes)](https://jbrowse.org/jb2/docs/tutorials/sv_multisamples.md)
- [SVs (Cancer GIAB pt 1, breakpoints)](https://jbrowse.org/jb2/docs/tutorials/sv_visualization_cgiab.md)
- [SVs (Cancer GIAB pt 2, copy number)](https://jbrowse.org/jb2/docs/tutorials/cnv_cgiab.md)
- [SVs (complex rearrangements)](https://jbrowse.org/jb2/docs/tutorials/cancer_sv.md)
- [SVs (gene fusion calls)](https://jbrowse.org/jb2/docs/tutorials/k562_fusions.md)
- [SVs from Hi-C](https://jbrowse.org/jb2/docs/tutorials/hic_structural_variants.md)
- [Synteny (all-vs-all minimap2)](https://jbrowse.org/jb2/docs/tutorials/allvsall_synteny.md)
- [Synteny (ancestral linkage groups)](https://jbrowse.org/jb2/docs/tutorials/odp_linkage_groups_synteny.md)
- [Synteny (Cactus lanes, apes)](https://jbrowse.org/jb2/docs/tutorials/t2t_apes_cactus_synteny.md)
- [Synteny (circular, human and mouse)](https://jbrowse.org/jb2/docs/tutorials/circular_synteny.md)
- [Synteny (dN/dS)](https://jbrowse.org/jb2/docs/tutorials/selection_pressure.md)
- [Synteny (gene-symbol lanes, bacteria)](https://jbrowse.org/jb2/docs/tutorials/ecoli_orthologs_synteny.md)
- [Synteny (gene-symbol lanes)](https://jbrowse.org/jb2/docs/tutorials/primate_orthologs_synteny.md)
- [Synteny (haplotypes, T2T-HG002)](https://jbrowse.org/jb2/docs/tutorials/hg002_haplotypes.md)
- [Synteny (liftOver lanes, vertebrates)](https://jbrowse.org/jb2/docs/tutorials/hg38_vertebrates_synteny.md)
- [Synteny (MCScan anchors)](https://jbrowse.org/jb2/docs/tutorials/mcscan_synteny_grape_peach.md)
- [Synteny (OrthoFinder)](https://jbrowse.org/jb2/docs/tutorials/orthofinder_synteny.md)
- [Synteny (ortholog tables)](https://jbrowse.org/jb2/docs/tutorials/multiway_synteny_grape_peach_cacao.md)
- [Synteny (pairwise minimap2)](https://jbrowse.org/jb2/docs/tutorials/synteny_visualization.md)
- [Synteny (polyploid subgenomes)](https://jbrowse.org/jb2/docs/tutorials/homoeolog_synteny.md)
- [Synteny (SyRI rearrangement types)](https://jbrowse.org/jb2/docs/tutorials/syri_synteny.md)

## Configuration

The config model: assemblies, then tracks; each track = one adapter (data) + display type(s), wired with JEXL. Per-type slots are under "Reference: Config schema".

- [Configuration](https://jbrowse.org/jb2/docs/config_guide.md)
- [Config and session JSON](https://jbrowse.org/jb2/docs/automating.md)
- [URL parameters](https://jbrowse.org/jb2/docs/urlparams.md)
- [Core configuration: config.json format](https://jbrowse.org/jb2/docs/config_guides/intro.md)
- [Core configuration: Assemblies](https://jbrowse.org/jb2/docs/config_guides/assemblies.md)
- [Core configuration: Tracks](https://jbrowse.org/jb2/docs/config_guides/tracks.md)
- [Core configuration: Authentication](https://jbrowse.org/jb2/docs/config_guides/authentication.md)
- [Core configuration: Config slot types](https://jbrowse.org/jb2/docs/config_guides/slot_types.md)
- [Core configuration: Connections](https://jbrowse.org/jb2/docs/config_guides/connections.md)
- [Core configuration: FromConfig adapters](https://jbrowse.org/jb2/docs/config_guides/from_config.md)
- [Core configuration: Plugins](https://jbrowse.org/jb2/docs/config_guides/plugins.md)
- [Core configuration: Supported file types](https://jbrowse.org/jb2/docs/config_guides/file_types.md)
- [Core configuration: Text searching](https://jbrowse.org/jb2/docs/config_guides/text_searching.md)
- [Track types: Alignments track](https://jbrowse.org/jb2/docs/config_guides/alignments_track.md)
- [Track types: Grouping and lane order](https://jbrowse.org/jb2/docs/config_guides/grouping_and_ordering.md)
- [Track types: GWAS track](https://jbrowse.org/jb2/docs/config_guides/gwas_track.md)
- [Track types: Hi-C track](https://jbrowse.org/jb2/docs/config_guides/hic_track.md)
- [Track types: MAF track](https://jbrowse.org/jb2/docs/config_guides/maf_track.md)
- [Track types: Mark display](https://jbrowse.org/jb2/docs/config_guides/mark_display.md)
- [Track types: Mark display examples](https://jbrowse.org/jb2/docs/config_guides/mark_display_examples.md)
- [Track types: Quantitative track](https://jbrowse.org/jb2/docs/config_guides/quantitative_track.md)
- [Track types: Synteny track](https://jbrowse.org/jb2/docs/config_guides/synteny_track.md)
- [Track types: Variant track](https://jbrowse.org/jb2/docs/config_guides/variant_track.md)
- [Callbacks: Customizing feature colors](https://jbrowse.org/jb2/docs/config_guides/customizing_feature_colors.md)
- [Callbacks: Customizing feature details](https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details.md)
- [Callbacks: Using jexl callbacks](https://jbrowse.org/jb2/docs/config_guides/jexl.md)
- [Appearance: Coloring/theming](https://jbrowse.org/jb2/docs/config_guides/theme.md)
- [Appearance: Default session](https://jbrowse.org/jb2/docs/config_guides/default_session.md)
- [Appearance: Hierarchical track selector](https://jbrowse.org/jb2/docs/config_guides/track_selector.md)
- [Deployment: Avoiding stale config](https://jbrowse.org/jb2/docs/config_guides/avoiding_stale_config.md)
- [Deployment: Deploying JBrowse Web](https://jbrowse.org/jb2/docs/config_guides/deploying.md)
- [Deployment: Disabling analytics](https://jbrowse.org/jb2/docs/config_guides/disable_analytics.md)
- [Deployment: Serving data files](https://jbrowse.org/jb2/docs/config_guides/serving_data.md)

## Development

- [Development](https://jbrowse.org/jb2/docs/developer_guide.md)
- [Getting started: Writing a plugin](https://jbrowse.org/jb2/docs/developer_guides/simple_plugin.md)
- [Getting started: Writing a no-build plugin](https://jbrowse.org/jb2/docs/developer_guides/no_build_plugin.md)
- [Getting started: Pluggable elements](https://jbrowse.org/jb2/docs/developer_guides/pluggable_elements.md)
- [Plugins: Tracks and displays](https://jbrowse.org/jb2/docs/developer_guides/creating_display.md)
- [Plugins: Plotting features](https://jbrowse.org/jb2/docs/developer_guides/plotting_features.md)
- [Plugins: GPU displays](https://jbrowse.org/jb2/docs/developer_guides/creating_gpu_display.md)
- [Plugins: Add-track workflows](https://jbrowse.org/jb2/docs/developer_guides/creating_addtrack_workflow.md)
- [Plugins: Custom adapters](https://jbrowse.org/jb2/docs/developer_guides/creating_adapter.md)
- [Plugins: Custom connections](https://jbrowse.org/jb2/docs/developer_guides/creating_connection.md)
- [Plugins: Custom view types](https://jbrowse.org/jb2/docs/developer_guides/creating_view.md)
- [Plugins: Custom widgets](https://jbrowse.org/jb2/docs/developer_guides/creating_widget.md)
- [Plugins: Drawer widgets](https://jbrowse.org/jb2/docs/developer_guides/drawer_widgets.md)
- [Plugins: Load cost](https://jbrowse.org/jb2/docs/developer_guides/plugin_load_cost.md)
- [Plugins: Menus](https://jbrowse.org/jb2/docs/developer_guides/menus.md)
- [Plugins: SVG export](https://jbrowse.org/jb2/docs/developer_guides/svg_export.md)
- [Plugins: Text search adapters](https://jbrowse.org/jb2/docs/developer_guides/creating_text_search_adapter.md)
- [Plugins: Upgrading to v5](https://jbrowse.org/jb2/docs/developer_guides/upgrading_v5.md)
- [Core concepts: Configuration schema](https://jbrowse.org/jb2/docs/developer_guides/configuration_schema.md)
- [Core concepts: Data fetching pipeline](https://jbrowse.org/jb2/docs/developer_guides/data_fetching.md)
- [Core concepts: Data flow, end to end](https://jbrowse.org/jb2/docs/developer_guides/dataflow.md)
- [Core concepts: Dependencies and re-exports](https://jbrowse.org/jb2/docs/developer_guides/imports_and_reexports.md)
- [Core concepts: Extension points](https://jbrowse.org/jb2/docs/developer_guides/extension_points.md)
- [Core concepts: MST patterns](https://jbrowse.org/jb2/docs/developer_guides/mst_patterns.md)
- [Core concepts: RPC and worker system](https://jbrowse.org/jb2/docs/developer_guides/rpc_workers.md)
- [Advanced topics: Memory and retention](https://jbrowse.org/jb2/docs/developer_guides/memory.md)
- [Advanced topics: Optimizations](https://jbrowse.org/jb2/docs/developer_guides/optimizations.md)
- [Advanced topics: PIF format](https://jbrowse.org/jb2/docs/developer_guides/pif_format.md)
- [Advanced topics: RefName aliasing](https://jbrowse.org/jb2/docs/developer_guides/refname_aliasing.md)
- [Advanced topics: Testing a plugin](https://jbrowse.org/jb2/docs/developer_guides/testing_plugins.md)
- [Advanced topics: Theming](https://jbrowse.org/jb2/docs/developer_guides/theming.md)
- [Advanced topics: Why not deck.gl, Pixi, Rust or wgpu](https://jbrowse.org/jb2/docs/developer_guides/why_not_x.md)

## Reference: Config schema

Generated config-slot reference per adapter/track/display type (BamAdapter, LinearWiggleDisplay, ...). Fetch the page for the type you are configuring.

- [Reference: Config schema](https://jbrowse.org/jb2/docs/config.md)
- [Adapter: BamAdapter](https://jbrowse.org/jb2/docs/config/bamadapter.md)
- [Adapter: BamIndex](https://jbrowse.org/jb2/docs/config/bamindex.md)
- [Adapter: BedAdapter](https://jbrowse.org/jb2/docs/config/bedadapter.md)
- [Adapter: BedGraphAdapter](https://jbrowse.org/jb2/docs/config/bedgraphadapter.md)
- [Adapter: BedGraphTabixAdapter](https://jbrowse.org/jb2/docs/config/bedgraphtabixadapter.md)
- [Adapter: BedpeAdapter](https://jbrowse.org/jb2/docs/config/bedpeadapter.md)
- [Adapter: BedTabixAdapter](https://jbrowse.org/jb2/docs/config/bedtabixadapter.md)
- [Adapter: BgzipFastaAdapter](https://jbrowse.org/jb2/docs/config/bgzipfastaadapter.md)
- [Adapter: BgzipMafAdapter](https://jbrowse.org/jb2/docs/config/bgzipmafadapter.md)
- [Adapter: BgzipTaffyAdapter](https://jbrowse.org/jb2/docs/config/bgziptaffyadapter.md)
- [Adapter: BigBedAdapter](https://jbrowse.org/jb2/docs/config/bigbedadapter.md)
- [Adapter: BigBedTextSearchAdapter](https://jbrowse.org/jb2/docs/config/bigbedtextsearchadapter.md)
- [Adapter: BigMafAdapter](https://jbrowse.org/jb2/docs/config/bigmafadapter.md)
- [Adapter: BigWigAdapter](https://jbrowse.org/jb2/docs/config/bigwigadapter.md)
- [Adapter: BlastTabularAdapter](https://jbrowse.org/jb2/docs/config/blasttabularadapter.md)
- [Adapter: ChainAdapter](https://jbrowse.org/jb2/docs/config/chainadapter.md)
- [Adapter: ChromSizesAdapter](https://jbrowse.org/jb2/docs/config/chromsizesadapter.md)
- [Adapter: CramAdapter](https://jbrowse.org/jb2/docs/config/cramadapter.md)
- [Adapter: CrisprGuideAdapter](https://jbrowse.org/jb2/docs/config/crisprguideadapter.md)
- [Adapter: CytobandAdapter](https://jbrowse.org/jb2/docs/config/cytobandadapter.md)
- [Adapter: DeltaAdapter](https://jbrowse.org/jb2/docs/config/deltaadapter.md)
- [Adapter: FromConfigAdapter](https://jbrowse.org/jb2/docs/config/fromconfigadapter.md)
- [Adapter: FromConfigRegionsAdapter](https://jbrowse.org/jb2/docs/config/fromconfigregionsadapter.md)
- [Adapter: FromConfigSequenceAdapter](https://jbrowse.org/jb2/docs/config/fromconfigsequenceadapter.md)
- [Adapter: GCContentAdapter](https://jbrowse.org/jb2/docs/config/gccontentadapter.md)
- [Adapter: Gff3Adapter](https://jbrowse.org/jb2/docs/config/gff3adapter.md)
- [Adapter: Gff3TabixAdapter](https://jbrowse.org/jb2/docs/config/gff3tabixadapter.md)
- [Adapter: GtfAdapter](https://jbrowse.org/jb2/docs/config/gtfadapter.md)
- [Adapter: GtfTabixAdapter](https://jbrowse.org/jb2/docs/config/gtftabixadapter.md)
- [Adapter: GWASAdapter](https://jbrowse.org/jb2/docs/config/gwasadapter.md)
- [Adapter: HicAdapter](https://jbrowse.org/jb2/docs/config/hicadapter.md)
- [Adapter: HtsgetBamAdapter](https://jbrowse.org/jb2/docs/config/htsgetbamadapter.md)
- [Adapter: IndexedFastaAdapter](https://jbrowse.org/jb2/docs/config/indexedfastaadapter.md)
- [Adapter: JBrowse1TextSearchAdapter](https://jbrowse.org/jb2/docs/config/jbrowse1textsearchadapter.md)
- [Adapter: MafTabixAdapter](https://jbrowse.org/jb2/docs/config/maftabixadapter.md)
- [Adapter: MashMapAdapter](https://jbrowse.org/jb2/docs/config/mashmapadapter.md)
- [Adapter: MCScanAnchorsAdapter](https://jbrowse.org/jb2/docs/config/mcscananchorsadapter.md)
- [Adapter: MCScanBlocksAdapter](https://jbrowse.org/jb2/docs/config/mcscanblocksadapter.md)
- [Adapter: MCScanSimpleAnchorsAdapter](https://jbrowse.org/jb2/docs/config/mcscansimpleanchorsadapter.md)
- [Adapter: MotifListAdapter](https://jbrowse.org/jb2/docs/config/motiflistadapter.md)
- [Adapter: MultiGenomeIndexedPAFAdapter](https://jbrowse.org/jb2/docs/config/multigenomeindexedpafadapter.md)
- [Adapter: MultiGenomePAFAdapter](https://jbrowse.org/jb2/docs/config/multigenomepafadapter.md)
- [Adapter: MultiPairwiseSyntenyAdapter](https://jbrowse.org/jb2/docs/config/multipairwisesyntenyadapter.md)
- [Adapter: MultiWiggleAdapter](https://jbrowse.org/jb2/docs/config/multiwiggleadapter.md)
- [Adapter: NcbiSequenceReportAliasAdapter](https://jbrowse.org/jb2/docs/config/ncbisequencereportaliasadapter.md)
- [Adapter: NCListAdapter](https://jbrowse.org/jb2/docs/config/nclistadapter.md)
- [Adapter: PAFAdapter](https://jbrowse.org/jb2/docs/config/pafadapter.md)
- [Adapter: PairwiseIndexedPAFAdapter](https://jbrowse.org/jb2/docs/config/pairwiseindexedpafadapter.md)
- [Adapter: PlinkLDAdapter](https://jbrowse.org/jb2/docs/config/plinkldadapter.md)
- [Adapter: PlinkLDTabixAdapter](https://jbrowse.org/jb2/docs/config/plinkldtabixadapter.md)
- [Adapter: RefNameAliasAdapter](https://jbrowse.org/jb2/docs/config/refnamealiasadapter.md)
- [Adapter: SamAdapter](https://jbrowse.org/jb2/docs/config/samadapter.md)
- [Adapter: SequenceSearchAdapter](https://jbrowse.org/jb2/docs/config/sequencesearchadapter.md)
- [Adapter: SPARQLAdapter](https://jbrowse.org/jb2/docs/config/sparqladapter.md)
- [Adapter: SplitVcfTabixAdapter](https://jbrowse.org/jb2/docs/config/splitvcftabixadapter.md)
- [Adapter: StarFusionAdapter](https://jbrowse.org/jb2/docs/config/starfusionadapter.md)
- [Adapter: TabixIndex](https://jbrowse.org/jb2/docs/config/tabixindex.md)
- [Adapter: TrixTextSearchAdapter](https://jbrowse.org/jb2/docs/config/trixtextsearchadapter.md)
- [Adapter: TwoBitAdapter](https://jbrowse.org/jb2/docs/config/twobitadapter.md)
- [Adapter: UnindexedFastaAdapter](https://jbrowse.org/jb2/docs/config/unindexedfastaadapter.md)
- [Adapter: VcfAdapter](https://jbrowse.org/jb2/docs/config/vcfadapter.md)
- [Adapter: VcfTabixAdapter](https://jbrowse.org/jb2/docs/config/vcftabixadapter.md)
- [Assembly Management: BaseAssembly](https://jbrowse.org/jb2/docs/config/baseassembly.md)
- [Connection: BaseConnection](https://jbrowse.org/jb2/docs/config/baseconnection.md)
- [Connection: JB2TrackHubConnection](https://jbrowse.org/jb2/docs/config/jb2trackhubconnection.md)
- [Connection: JBrowse1Connection](https://jbrowse.org/jb2/docs/config/jbrowse1connection.md)
- [Connection: UCSCTrackHubConnection](https://jbrowse.org/jb2/docs/config/ucsctrackhubconnection.md)
- [Display: AlignmentsArcColor](https://jbrowse.org/jb2/docs/config/alignmentsarccolor.md)
- [Display: AlignmentsBaseColor](https://jbrowse.org/jb2/docs/config/alignmentsbasecolor.md)
- [Display: AlignmentsColor](https://jbrowse.org/jb2/docs/config/alignmentscolor.md)
- [Display: AlignmentsFilter](https://jbrowse.org/jb2/docs/config/alignmentsfilter.md)
- [Display: AlignmentsModifications](https://jbrowse.org/jb2/docs/config/alignmentsmodifications.md)
- [Display: AlignmentsSort](https://jbrowse.org/jb2/docs/config/alignmentssort.md)
- [Display: BaseAlignmentsFilter](https://jbrowse.org/jb2/docs/config/basealignmentsfilter.md)
- [Display: BaseLinearAlignmentsDisplay](https://jbrowse.org/jb2/docs/config/baselinearalignmentsdisplay.md)
- [Display: BaseLinearDisplay](https://jbrowse.org/jb2/docs/config/baselineardisplay.md)
- [Display: BasicFeatureFilter](https://jbrowse.org/jb2/docs/config/basicfeaturefilter.md)
- [Display: ChordColor](https://jbrowse.org/jb2/docs/config/chordcolor.md)
- [Display: ChordSyntenyDisplay](https://jbrowse.org/jb2/docs/config/chordsyntenydisplay.md)
- [Display: ChordVariantDisplay](https://jbrowse.org/jb2/docs/config/chordvariantdisplay.md)
- [Display: ConnectionFilter](https://jbrowse.org/jb2/docs/config/connectionfilter.md)
- [Display: CoverageBand](https://jbrowse.org/jb2/docs/config/coverageband.md)
- [Display: DotplotDisplay](https://jbrowse.org/jb2/docs/config/dotplotdisplay.md)
- [Display: Facet](https://jbrowse.org/jb2/docs/config/facet.md)
- [Display: FeatureColor](https://jbrowse.org/jb2/docs/config/featurecolor.md)
- [Display: FeatureFilter](https://jbrowse.org/jb2/docs/config/featurefilter.md)
- [Display: HicColor](https://jbrowse.org/jb2/docs/config/hiccolor.md)
- [Display: JunctionFilter](https://jbrowse.org/jb2/docs/config/junctionfilter.md)
- [Display: LaneRows](https://jbrowse.org/jb2/docs/config/lanerows.md)
- [Display: LDColor](https://jbrowse.org/jb2/docs/config/ldcolor.md)
- [Display: LDTrackDisplay](https://jbrowse.org/jb2/docs/config/ldtrackdisplay.md)
- [Display: LGVSyntenyColor](https://jbrowse.org/jb2/docs/config/lgvsyntenycolor.md)
- [Display: LGVSyntenyCoverage](https://jbrowse.org/jb2/docs/config/lgvsyntenycoverage.md)
- [Display: LGVSyntenyDisplay](https://jbrowse.org/jb2/docs/config/lgvsyntenydisplay.md)
- [Display: LGVSyntenySort](https://jbrowse.org/jb2/docs/config/lgvsyntenysort.md)
- [Display: LinearAlignmentsDisplay](https://jbrowse.org/jb2/docs/config/linearalignmentsdisplay.md)
- [Display: LinearBasicDisplay](https://jbrowse.org/jb2/docs/config/linearbasicdisplay.md)
- [Display: LinearCanvasBaseDisplay](https://jbrowse.org/jb2/docs/config/linearcanvasbasedisplay.md)
- [Display: LinearHicDisplay](https://jbrowse.org/jb2/docs/config/linearhicdisplay.md)
- [Display: LinearMafDisplay](https://jbrowse.org/jb2/docs/config/linearmafdisplay.md)
- [Display: LinearManhattanDisplay](https://jbrowse.org/jb2/docs/config/linearmanhattandisplay.md)
- [Display: LinearMarkDisplay](https://jbrowse.org/jb2/docs/config/linearmarkdisplay.md)
- [Display: LinearMultiRowFeatureDisplay](https://jbrowse.org/jb2/docs/config/linearmultirowfeaturedisplay.md)
- [Display: LinearMultiSampleVariantDisplay](https://jbrowse.org/jb2/docs/config/linearmultisamplevariantdisplay.md)
- [Display: LinearReferenceSequenceDisplay](https://jbrowse.org/jb2/docs/config/linearreferencesequencedisplay.md)
- [Display: LinearScoreDisplay](https://jbrowse.org/jb2/docs/config/linearscoredisplay.md)
- [Display: LinearSyntenyDisplay](https://jbrowse.org/jb2/docs/config/linearsyntenydisplay.md)
- [Display: LinearVariantDisplay](https://jbrowse.org/jb2/docs/config/linearvariantdisplay.md)
- [Display: LinearWiggleDisplay](https://jbrowse.org/jb2/docs/config/linearwiggledisplay.md)
- [Display: MafAlignments](https://jbrowse.org/jb2/docs/config/mafalignments.md)
- [Display: MafColor](https://jbrowse.org/jb2/docs/config/mafcolor.md)
- [Display: MafConservation](https://jbrowse.org/jb2/docs/config/mafconservation.md)
- [Display: MarkColor](https://jbrowse.org/jb2/docs/config/markcolor.md)
- [Display: MarkFacet](https://jbrowse.org/jb2/docs/config/markfacet.md)
- [Display: MarkLocus](https://jbrowse.org/jb2/docs/config/marklocus.md)
- [Display: MarkSize](https://jbrowse.org/jb2/docs/config/marksize.md)
- [Display: MarkTransform](https://jbrowse.org/jb2/docs/config/marktransform.md)
- [Display: MultiWayGeneColor](https://jbrowse.org/jb2/docs/config/multiwaygenecolor.md)
- [Display: MultiWayLaneLayer](https://jbrowse.org/jb2/docs/config/multiwaylanelayer.md)
- [Display: MultiWaySyntenyDisplay](https://jbrowse.org/jb2/docs/config/multiwaysyntenydisplay.md)
- [Display: Pileup](https://jbrowse.org/jb2/docs/config/pileup.md)
- [Display: QuantitativeRows](https://jbrowse.org/jb2/docs/config/quantitativerows.md)
- [Display: ReadConnections](https://jbrowse.org/jb2/docs/config/readconnections.md)
- [Display: RibbonColor](https://jbrowse.org/jb2/docs/config/ribboncolor.md)
- [Display: RowArrangement](https://jbrowse.org/jb2/docs/config/rowarrangement.md)
- [Display: RowColor](https://jbrowse.org/jb2/docs/config/rowcolor.md)
- [Display: RowGroup](https://jbrowse.org/jb2/docs/config/rowgroup.md)
- [Display: Rows](https://jbrowse.org/jb2/docs/config/rows.md)
- [Display: SampleRows](https://jbrowse.org/jb2/docs/config/samplerows.md)
- [Display: Sashimi](https://jbrowse.org/jb2/docs/config/sashimi.md)
- [Display: SectionFacet](https://jbrowse.org/jb2/docs/config/sectionfacet.md)
- [Display: TagFilter](https://jbrowse.org/jb2/docs/config/tagfilter.md)
- [Display: ValueScale](https://jbrowse.org/jb2/docs/config/valuescale.md)
- [Display: VariantCellColor](https://jbrowse.org/jb2/docs/config/variantcellcolor.md)
- [Display: VariantFilter](https://jbrowse.org/jb2/docs/config/variantfilter.md)
- [Display: VariantsBand](https://jbrowse.org/jb2/docs/config/variantsband.md)
- [Display: WiggleColor](https://jbrowse.org/jb2/docs/config/wigglecolor.md)
- [Internet Account: BaseInternetAccount](https://jbrowse.org/jb2/docs/config/baseinternetaccount.md)
- [Internet Account: DropboxOAuthInternetAccount](https://jbrowse.org/jb2/docs/config/dropboxoauthinternetaccount.md)
- [Internet Account: ExternalTokenInternetAccount](https://jbrowse.org/jb2/docs/config/externaltokeninternetaccount.md)
- [Internet Account: GoogleDriveOAuthInternetAccount](https://jbrowse.org/jb2/docs/config/googledriveoauthinternetaccount.md)
- [Internet Account: HTTPBasicInternetAccount](https://jbrowse.org/jb2/docs/config/httpbasicinternetaccount.md)
- [Internet Account: OAuthInternetAccount](https://jbrowse.org/jb2/docs/config/oauthinternetaccount.md)
- [Root: FormatAbout](https://jbrowse.org/jb2/docs/config/formatabout.md)
- [Root: FormatDetails](https://jbrowse.org/jb2/docs/config/formatdetails.md)
- [Root: HierarchicalConfigSchema](https://jbrowse.org/jb2/docs/config/hierarchicalconfigschema.md)
- [Root: JBrowseConfiguration](https://jbrowse.org/jb2/docs/config/jbrowseconfiguration.md)
- [Root: JBrowseRootConfig](https://jbrowse.org/jb2/docs/config/jbrowserootconfig.md)
- [Root: LinearGenomeViewConfigSchema](https://jbrowse.org/jb2/docs/config/lineargenomeviewconfigschema.md)
- [Root: PreferencesConfigSchema](https://jbrowse.org/jb2/docs/config/preferencesconfigschema.md)
- [Root: RpcOptions](https://jbrowse.org/jb2/docs/config/rpcoptions.md)
- [Track: AlignmentsTrack](https://jbrowse.org/jb2/docs/config/alignmentstrack.md)
- [Track: BaseTrack](https://jbrowse.org/jb2/docs/config/basetrack.md)
- [Track: FeatureTrack](https://jbrowse.org/jb2/docs/config/featuretrack.md)
- [Track: GCContentTrack](https://jbrowse.org/jb2/docs/config/gccontenttrack.md)
- [Track: GWASTrack](https://jbrowse.org/jb2/docs/config/gwastrack.md)
- [Track: HicTrack](https://jbrowse.org/jb2/docs/config/hictrack.md)
- [Track: LDTrack](https://jbrowse.org/jb2/docs/config/ldtrack.md)
- [Track: MafTrack](https://jbrowse.org/jb2/docs/config/maftrack.md)
- [Track: MultiQuantitativeTrack](https://jbrowse.org/jb2/docs/config/multiquantitativetrack.md)
- [Track: QuantitativeTrack](https://jbrowse.org/jb2/docs/config/quantitativetrack.md)
- [Track: ReferenceSequenceTrack](https://jbrowse.org/jb2/docs/config/referencesequencetrack.md)
- [Track: SyntenyTrack](https://jbrowse.org/jb2/docs/config/syntenytrack.md)
- [Track: VariantTrack](https://jbrowse.org/jb2/docs/config/varianttrack.md)
- [View: SyntenyColor](https://jbrowse.org/jb2/docs/config/syntenycolor.md)
- [View: SyntenyOpacity](https://jbrowse.org/jb2/docs/config/syntenyopacity.md)

## Reference: State models

Generated reference for the MobX state-tree models behind each view, display, and session: the properties, actions, and getters a plugin can call.

- [Reference: State models](https://jbrowse.org/jb2/docs/models.md)
- [Assembly Management: Assembly](https://jbrowse.org/jb2/docs/models/assembly.md)
- [Assembly Management: AssemblyManager](https://jbrowse.org/jb2/docs/models/assemblymanager.md)
- [Connection: BaseConnectionModel](https://jbrowse.org/jb2/docs/models/baseconnectionmodel.md)
- [Connection: JB2TrackHubConnection](https://jbrowse.org/jb2/docs/models/jb2trackhubconnection.md)
- [Connection: JBrowse1Connection](https://jbrowse.org/jb2/docs/models/jbrowse1connection.md)
- [Connection: UCSCTrackHubConnection](https://jbrowse.org/jb2/docs/models/ucsctrackhubconnection.md)
- [Display: BaseChordDisplay](https://jbrowse.org/jb2/docs/models/basechorddisplay.md)
- [Display: BaseDisplay](https://jbrowse.org/jb2/docs/models/basedisplay.md)
- [Display: ChordSyntenyDisplay](https://jbrowse.org/jb2/docs/models/chordsyntenydisplay.md)
- [Display: ChordVariantDisplay](https://jbrowse.org/jb2/docs/models/chordvariantdisplay.md)
- [Display: DotplotDisplay](https://jbrowse.org/jb2/docs/models/dotplotdisplay.md)
- [Display: LDTrackDisplay](https://jbrowse.org/jb2/docs/models/ldtrackdisplay.md)
- [Display: LGVSyntenyDisplay](https://jbrowse.org/jb2/docs/models/lgvsyntenydisplay.md)
- [Display: LinearAlignmentsDisplay](https://jbrowse.org/jb2/docs/models/linearalignmentsdisplay.md)
- [Display: LinearBasicDisplay](https://jbrowse.org/jb2/docs/models/linearbasicdisplay.md)
- [Display: LinearCanvasBaseDisplay](https://jbrowse.org/jb2/docs/models/linearcanvasbasedisplay.md)
- [Display: LinearHicDisplay](https://jbrowse.org/jb2/docs/models/linearhicdisplay.md)
- [Display: LinearMafDisplay](https://jbrowse.org/jb2/docs/models/linearmafdisplay.md)
- [Display: LinearManhattanDisplay](https://jbrowse.org/jb2/docs/models/linearmanhattandisplay.md)
- [Display: LinearMarkDisplay](https://jbrowse.org/jb2/docs/models/linearmarkdisplay.md)
- [Display: LinearMultiRowFeatureDisplay](https://jbrowse.org/jb2/docs/models/linearmultirowfeaturedisplay.md)
- [Display: LinearMultiSampleVariantDisplay](https://jbrowse.org/jb2/docs/models/linearmultisamplevariantdisplay.md)
- [Display: LinearReferenceSequenceDisplay](https://jbrowse.org/jb2/docs/models/linearreferencesequencedisplay.md)
- [Display: LinearScoreDisplay](https://jbrowse.org/jb2/docs/models/linearscoredisplay.md)
- [Display: LinearSyntenyDisplay](https://jbrowse.org/jb2/docs/models/linearsyntenydisplay.md)
- [Display: LinearVariantDisplay](https://jbrowse.org/jb2/docs/models/linearvariantdisplay.md)
- [Display: LinearWiggleDisplay](https://jbrowse.org/jb2/docs/models/linearwiggledisplay.md)
- [Display: MultiWaySyntenyDisplay](https://jbrowse.org/jb2/docs/models/multiwaysyntenydisplay.md)
- [General: Base1DView](https://jbrowse.org/jb2/docs/models/base1dview.md)
- [General: Dotplot1DView](https://jbrowse.org/jb2/docs/models/dotplot1dview.md)
- [General: LinearSyntenyViewHelper](https://jbrowse.org/jb2/docs/models/linearsyntenyviewhelper.md)
- [General: TimeTraveller](https://jbrowse.org/jb2/docs/models/timetraveller.md)
- [Internet Account: BaseInternetAccountModel](https://jbrowse.org/jb2/docs/models/baseinternetaccountmodel.md)
- [Internet Account: DropboxOAuthInternetAccount](https://jbrowse.org/jb2/docs/models/dropboxoauthinternetaccount.md)
- [Internet Account: ExternalTokenInternetAccount](https://jbrowse.org/jb2/docs/models/externaltokeninternetaccount.md)
- [Internet Account: GoogleDriveOAuthInternetAccount](https://jbrowse.org/jb2/docs/models/googledriveoauthinternetaccount.md)
- [Internet Account: HTTPBasicInternetAccount](https://jbrowse.org/jb2/docs/models/httpbasicinternetaccount.md)
- [Internet Account: OAuthInternetAccount](https://jbrowse.org/jb2/docs/models/oauthinternetaccount.md)
- [Internet Account: TokenEntryInternetAccount](https://jbrowse.org/jb2/docs/models/tokenentryinternetaccount.md)
- [Mixin: AppSessionMixin](https://jbrowse.org/jb2/docs/models/appsessionmixin.md)
- [Mixin: AssembliesMixin](https://jbrowse.org/jb2/docs/models/assembliesmixin.md)
- [Mixin: CanvasFeatureGateMixin](https://jbrowse.org/jb2/docs/models/canvasfeaturegatemixin.md)
- [Mixin: CoarseTierMixin](https://jbrowse.org/jb2/docs/models/coarsetiermixin.md)
- [Mixin: ColorWritesMixin](https://jbrowse.org/jb2/docs/models/colorwritesmixin.md)
- [Mixin: ComparativeFetchMixin](https://jbrowse.org/jb2/docs/models/comparativefetchmixin.md)
- [Mixin: ConnectionManagementSessionMixin](https://jbrowse.org/jb2/docs/models/connectionmanagementsessionmixin.md)
- [Mixin: ContextMenuMixin](https://jbrowse.org/jb2/docs/models/contextmenumixin.md)
- [Mixin: DesktopSessionTrackMenuMixin](https://jbrowse.org/jb2/docs/models/desktopsessiontrackmenumixin.md)
- [Mixin: DiagonalizeProgressMixin](https://jbrowse.org/jb2/docs/models/diagonalizeprogressmixin.md)
- [Mixin: DrawerWidgetSessionMixin](https://jbrowse.org/jb2/docs/models/drawerwidgetsessionmixin.md)
- [Mixin: EmbeddedSessionMixin](https://jbrowse.org/jb2/docs/models/embeddedsessionmixin.md)
- [Mixin: EmbeddedSessionThemeMixin](https://jbrowse.org/jb2/docs/models/embeddedsessionthememixin.md)
- [Mixin: FacetWritesMixin](https://jbrowse.org/jb2/docs/models/facetwritesmixin.md)
- [Mixin: FetchMixin](https://jbrowse.org/jb2/docs/models/fetchmixin.md)
- [Mixin: GlobalFetchMixin](https://jbrowse.org/jb2/docs/models/globalfetchmixin.md)
- [Mixin: HeightModeMixin](https://jbrowse.org/jb2/docs/models/heightmodemixin.md)
- [Mixin: HiddenGroupsMixin](https://jbrowse.org/jb2/docs/models/hiddengroupsmixin.md)
- [Mixin: HistoryManagementMixin](https://jbrowse.org/jb2/docs/models/historymanagementmixin.md)
- [Mixin: ImportFormSyntenyMixin](https://jbrowse.org/jb2/docs/models/importformsyntenymixin.md)
- [Mixin: InternetAccountsMixin](https://jbrowse.org/jb2/docs/models/internetaccountsmixin.md)
- [Mixin: KeyedFetchMixin](https://jbrowse.org/jb2/docs/models/keyedfetchmixin.md)
- [Mixin: LegendMixin](https://jbrowse.org/jb2/docs/models/legendmixin.md)
- [Mixin: LodTierInfoMixin](https://jbrowse.org/jb2/docs/models/lodtierinfomixin.md)
- [Mixin: MultipleViewsSessionMixin](https://jbrowse.org/jb2/docs/models/multipleviewssessionmixin.md)
- [Mixin: MultiRegionDisplayMixin](https://jbrowse.org/jb2/docs/models/multiregiondisplaymixin.md)
- [Mixin: PointerHoverMixin](https://jbrowse.org/jb2/docs/models/pointerhovermixin.md)
- [Mixin: PreferencesSessionMixin](https://jbrowse.org/jb2/docs/models/preferencessessionmixin.md)
- [Mixin: ReferenceManagementSessionMixin](https://jbrowse.org/jb2/docs/models/referencemanagementsessionmixin.md)
- [Mixin: RegionTooLargeMixin](https://jbrowse.org/jb2/docs/models/regiontoolargemixin.md)
- [Mixin: RenderLifecycleMixin](https://jbrowse.org/jb2/docs/models/renderlifecyclemixin.md)
- [Mixin: RootAppMenuMixin](https://jbrowse.org/jb2/docs/models/rootappmenumixin.md)
- [Mixin: RowHeightMixin](https://jbrowse.org/jb2/docs/models/rowheightmixin.md)
- [Mixin: ScoreAxisMixin](https://jbrowse.org/jb2/docs/models/scoreaxismixin.md)
- [Mixin: ScoreScaleMixin](https://jbrowse.org/jb2/docs/models/scorescalemixin.md)
- [Mixin: SessionTracksManagerSessionMixin](https://jbrowse.org/jb2/docs/models/sessiontracksmanagersessionmixin.md)
- [Mixin: StoredHoverMixin](https://jbrowse.org/jb2/docs/models/storedhovermixin.md)
- [Mixin: SyntenyColorsMixin](https://jbrowse.org/jb2/docs/models/syntenycolorsmixin.md)
- [Mixin: SyntenyFadeMixin](https://jbrowse.org/jb2/docs/models/syntenyfademixin.md)
- [Mixin: SyntenyViewMixin](https://jbrowse.org/jb2/docs/models/syntenyviewmixin.md)
- [Mixin: ThemeManagerSessionMixin](https://jbrowse.org/jb2/docs/models/thememanagersessionmixin.md)
- [Mixin: TrackColorsMixin](https://jbrowse.org/jb2/docs/models/trackcolorsmixin.md)
- [Mixin: TrackHeightMixin](https://jbrowse.org/jb2/docs/models/trackheightmixin.md)
- [Mixin: TrackMenuItemsSessionMixin](https://jbrowse.org/jb2/docs/models/trackmenuitemssessionmixin.md)
- [Mixin: TrackMenuSessionMixin](https://jbrowse.org/jb2/docs/models/trackmenusessionmixin.md)
- [Mixin: TracksManagerSessionMixin](https://jbrowse.org/jb2/docs/models/tracksmanagersessionmixin.md)
- [Mixin: TreeSidebarMixin](https://jbrowse.org/jb2/docs/models/treesidebarmixin.md)
- [Mixin: TriangleMatrixMixin](https://jbrowse.org/jb2/docs/models/trianglematrixmixin.md)
- [Mixin: WebSessionConnectionsMixin](https://jbrowse.org/jb2/docs/models/websessionconnectionsmixin.md)
- [Mixin: WebSessionManagementMixin](https://jbrowse.org/jb2/docs/models/websessionmanagementmixin.md)
- [Mixin: WiggleCommonMixin](https://jbrowse.org/jb2/docs/models/wigglecommonmixin.md)
- [Mixin: WiggleScoreConfigMixin](https://jbrowse.org/jb2/docs/models/wigglescoreconfigmixin.md)
- [Mixin: WorkspaceLayoutMixin](https://jbrowse.org/jb2/docs/models/workspacelayoutmixin.md)
- [Mixin: YFieldConfigMixin](https://jbrowse.org/jb2/docs/models/yfieldconfigmixin.md)
- [Root: AppCoreJBrowseModel](https://jbrowse.org/jb2/docs/models/appcorejbrowsemodel.md)
- [Root: BaseRootModel](https://jbrowse.org/jb2/docs/models/baserootmodel.md)
- [Root: EmbeddedRootModel](https://jbrowse.org/jb2/docs/models/embeddedrootmodel.md)
- [Root: JBrowseDesktopConfigModel](https://jbrowse.org/jb2/docs/models/jbrowsedesktopconfigmodel.md)
- [Root: JBrowseDesktopRootModel](https://jbrowse.org/jb2/docs/models/jbrowsedesktoprootmodel.md)
- [Root: JBrowseReactAppRootModel](https://jbrowse.org/jb2/docs/models/jbrowsereactapprootmodel.md)
- [Root: JBrowseReactLinearGenomeViewRootModel](https://jbrowse.org/jb2/docs/models/jbrowsereactlineargenomeviewrootmodel.md)
- [Root: JBrowseWebRootModel](https://jbrowse.org/jb2/docs/models/jbrowsewebrootmodel.md)
- [Session: BaseSessionModel](https://jbrowse.org/jb2/docs/models/basesessionmodel.md)
- [Session: BaseWebSessionModel](https://jbrowse.org/jb2/docs/models/basewebsessionmodel.md)
- [Session: JBrowseDesktopSessionModel](https://jbrowse.org/jb2/docs/models/jbrowsedesktopsessionmodel.md)
- [Session: JBrowseReactCircularGenomeViewSessionModel](https://jbrowse.org/jb2/docs/models/jbrowsereactcirculargenomeviewsessionmodel.md)
- [Session: JBrowseReactLinearGenomeViewSessionModel](https://jbrowse.org/jb2/docs/models/jbrowsereactlineargenomeviewsessionmodel.md)
- [Session: JBrowseWebSessionModel](https://jbrowse.org/jb2/docs/models/jbrowsewebsessionmodel.md)
- [Session: SnackbarModel](https://jbrowse.org/jb2/docs/models/snackbarmodel.md)
- [Track: BaseTrackModel](https://jbrowse.org/jb2/docs/models/basetrackmodel.md)
- [View: BaseViewModel](https://jbrowse.org/jb2/docs/models/baseviewmodel.md)
- [View: BreakpointSplitView](https://jbrowse.org/jb2/docs/models/breakpointsplitview.md)
- [View: CircularView](https://jbrowse.org/jb2/docs/models/circularview.md)
- [View: DotplotView](https://jbrowse.org/jb2/docs/models/dotplotview.md)
- [View: LinearGenomeView](https://jbrowse.org/jb2/docs/models/lineargenomeview.md)
- [View: LinearSyntenyView](https://jbrowse.org/jb2/docs/models/linearsyntenyview.md)
- [View: SpreadsheetView](https://jbrowse.org/jb2/docs/models/spreadsheetview.md)
- [View: SvInspectorView](https://jbrowse.org/jb2/docs/models/svinspectorview.md)
- [Widget: AddTrackModel](https://jbrowse.org/jb2/docs/models/addtrackmodel.md)
- [Widget: BaseFeatureWidget](https://jbrowse.org/jb2/docs/models/basefeaturewidget.md)
- [Widget: ConfigurationEditorWidget](https://jbrowse.org/jb2/docs/models/configurationeditorwidget.md)
- [Widget: GridBookmarkWidgetModel](https://jbrowse.org/jb2/docs/models/gridbookmarkwidgetmodel.md)
- [Widget: HierarchicalTrackSelectorWidget](https://jbrowse.org/jb2/docs/models/hierarchicaltrackselectorwidget.md)
- [Widget: MafSequenceWidget](https://jbrowse.org/jb2/docs/models/mafsequencewidget.md)
- [Widget: PluginStoreWidget](https://jbrowse.org/jb2/docs/models/pluginstorewidget.md)
- [Widget: ScoreAxisWidget](https://jbrowse.org/jb2/docs/models/scoreaxiswidget.md)
- [Widget: SequenceFeatureDetails](https://jbrowse.org/jb2/docs/models/sequencefeaturedetails.md)
- [Widget: SyntenyFeatureWidget](https://jbrowse.org/jb2/docs/models/syntenyfeaturewidget.md)
- [Widget: UcscResultsWidget](https://jbrowse.org/jb2/docs/models/ucscresultswidget.md)
- [Widget: VariantFeatureWidget](https://jbrowse.org/jb2/docs/models/variantfeaturewidget.md)

## Reference: Exported functions

- [Reference: Exported functions](https://jbrowse.org/jb2/docs/api.md)
- [@jbrowse/cigar-utils](https://jbrowse.org/jb2/docs/api/cigar-utils.md)
- [@jbrowse/core](https://jbrowse.org/jb2/docs/api/core.md)
- [@jbrowse/core (configuration)](https://jbrowse.org/jb2/docs/api/core-configuration.md)
- [@jbrowse/core (util)](https://jbrowse.org/jb2/docs/api/core-util.md)
- [@jbrowse/display-ui](https://jbrowse.org/jb2/docs/api/display-ui.md)
- [@jbrowse/modifications-utils](https://jbrowse.org/jb2/docs/api/modifications-utils.md)
- [@jbrowse/plugin-alignments](https://jbrowse.org/jb2/docs/api/alignments.md)
- [@jbrowse/plugin-canvas](https://jbrowse.org/jb2/docs/api/canvas.md)
- [@jbrowse/plugin-comparative-adapters](https://jbrowse.org/jb2/docs/api/comparative-adapters.md)
- [@jbrowse/plugin-config](https://jbrowse.org/jb2/docs/api/config.md)
- [@jbrowse/plugin-dotplot-view](https://jbrowse.org/jb2/docs/api/dotplot-view.md)
- [@jbrowse/plugin-linear-comparative-view](https://jbrowse.org/jb2/docs/api/linear-comparative-view.md)
- [@jbrowse/plugin-sequence](https://jbrowse.org/jb2/docs/api/sequence.md)
- [@jbrowse/plugin-variants](https://jbrowse.org/jb2/docs/api/variants.md)
- [@jbrowse/plugin-wiggle](https://jbrowse.org/jb2/docs/api/wiggle.md)
- [@jbrowse/sv-core](https://jbrowse.org/jb2/docs/api/sv-core.md)
- [@jbrowse/synteny-core](https://jbrowse.org/jb2/docs/api/synteny-core.md)
- [@jbrowse/wiggle-core](https://jbrowse.org/jb2/docs/api/wiggle-core.md)

## AI agents

Written for you. Driving a live JBrowse session from code, verified snippets for the common asks, hosted assemblies and tracks you can use with no setup, and how to screenshot a view and know it finished rendering.

- [AI agents](https://jbrowse.org/jb2/docs/agents.md)
- [Live model guide](https://jbrowse.org/jb2/docs/agents_live_model.md)
- [Recipes](https://jbrowse.org/jb2/docs/agents_recipes.md)
- [Hosted data](https://jbrowse.org/jb2/docs/agents_hosted_data.md)
- [Screenshots](https://jbrowse.org/jb2/docs/agents_capture.md)