GMOD · garrettjstevens · Jul 1, 2026 · Jun 26, 2026 · Jun 26, 2026 · Jun 30, 2026
diff --git a/packages/website/docs/01-user-guide/01-add-a-gene/apollo_annotation.png b/packages/website/docs/01-user-guide/01-add-a-gene/apollo_annotation.png
diff --git a/packages/website/docs/01-user-guide/01-add-a-gene/create_annotation_menu.png b/packages/website/docs/01-user-guide/01-add-a-gene/create_annotation_menu.png
diff --git a/packages/website/docs/01-user-guide/01-add-a-gene/index.md b/packages/website/docs/01-user-guide/01-add-a-gene/index.md
@@ -1,18 +1,22 @@
 # Add a gene
 
+Add a gene from a JBrowse evidence track.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 
 :::
 
-<a href="/demo//?assembly=Onchocerca%20volvulus&loc=OVOC_OM2:23836500-23840000&tracks=onchocerca_volvulus.PRJEB513.WBPS19.genomic-ReferenceSequenceTrack,apollo_track_Onchocerca%20volvulus,onchocerca_volvulus.PRJEB513.WBPS19.annotations.genes.sorted.gff3&tracklist=true"
+<a href="/demo//?assembly=Onchocerca%20volvulus&loc=OVOC_OM2:21267500-21270000&tracks=onchocerca_volvulus.PRJEB513.WBPS19.genomic-ReferenceSequenceTrack,apollo_track_Onchocerca%20volvulus,onchocerca_volvulus.PRJEB513.WBPS19.annotations.genes.sorted.gff3&tracklist=true"
 className="button button--primary button--lg" target="\_blank">Try
 it out</a>
 
+---
+
 Right-click on a gene in a JBrowse genes track and select "Create Apollo
 annotation" from the menu.
 

diff --git a/packages/website/docs/01-user-guide/01-add-a-gene/jbrowse_gene_context_menu.png b/packages/website/docs/01-user-guide/01-add-a-gene/jbrowse_gene_context_menu.png
diff --git a/packages/website/docs/01-user-guide/02-add-a-transcript/create_annotation_menu.png b/packages/website/docs/01-user-guide/02-add-a-transcript/create_annotation_menu.png
diff --git a/packages/website/docs/01-user-guide/02-add-a-transcript/index.md b/packages/website/docs/01-user-guide/02-add-a-transcript/index.md
@@ -1,10 +1,38 @@
 # Add a transcript
 
+Add a transcript from a JBrowse evidence gene track.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 
 :::
+
+<a href="/demo//?assembly=Onchocerca%20volvulus&loc=OVOC_OM2:23836500-23840000&tracks=onchocerca_volvulus.PRJEB513.WBPS19.genomic-ReferenceSequenceTrack,apollo_track_Onchocerca%20volvulus,onchocerca_volvulus.PRJEB513.WBPS19.annotations.genes.sorted.gff3&tracklist=true&apolloFeatures=H4sIAAAAAAAAA63WQW-bMBgG4L8yfWc0ge3YwG3tpJ22VOu0HqIIOeZLainY1JiuU8R_n4CtC6sCo-WE4LX1PjJgOMHaqHur0Cn57tEeH-tjXUG6OUGmc0iBS4qS0USEPMFVuIsFl5zTCAJwuL_FB0hh_X19na0_EwjA_ywRUjigQQig0AZSQmPKeUQCKORTf5pwGgZQeSdNDmkUgLrXx9yhgfR0oZEkbTZmIsm4qfj65cPCpmjSNLFO-GTNiIlzngxM0nund7XHqm0-7PdZZWunENIN3FlXXMkKYds0wSUPmRSTmWLB2bk4ZmRZMZ0U03nimPHwTBzzcLWsmE2K2UyxYOJcHLNwWfFqUryaKU4IP3-3wqWfCj4p5vPECRmKKY2WFYtJsZgpZiIa27_eLI4nxfG4-Prj7ZwN9__AQZe0qk1bkLa1gpJI_omMLLopg6B0mGvltTVZ5aXvPnFw01_EvB3xw7qixLKfeRMxkYh2dZrXuL45aSrldOn_8t5HF4F9tCTgExpM767aQxgSxiIa_tv-Mq3woUaj8AWwDXfa9nd1A6WzHrXJlM21OXQzbebRFc8ThyOy7m9gG4Cqnf7dfQEnj1pWw-qm2Ta_AFRAoM6lCAAA"
+className="button button--primary button--lg" target="\_blank">Try
+it out</a>
+
+---
+
+Here we see an Apollo annotation that has a single transcript, with a JBrowse
+evidence track that shows a second transcript. To add the second transcript to
+the Apollo annotation, start by right-clicking on the gene in the JBrowse track
+and selecting "Create Apollo annotation."
+
+![JBrowse gene context menu](jbrowse_gene_context_menu.png)
+
+In the dialog that appears, uncheck the gene and the first mRNA, since we only
+want to copy the second transcript. Make sure the gene in the destination
+feature drop-down box is the one to which we want to copy the transcript. Also
+make sure to not check the "Create new gene" box, since we're targeting an
+existing gene. Then click "Create."
+
+![Create annotation menu](create_annotation_menu.png)
+
+The transcript has now been added and is ready for any additional editing with
+Apollo.
+
+![Transcript has been added](transcript_added.png)
diff --git a/...es/website/docs/01-user-guide/02-add-a-transcript/jbrowse_gene_context_menu.png b/...es/website/docs/01-user-guide/02-add-a-transcript/jbrowse_gene_context_menu.png
diff --git a/packages/website/docs/01-user-guide/02-add-a-transcript/transcript_added.png b/packages/website/docs/01-user-guide/02-add-a-transcript/transcript_added.png
diff --git a/...bsite/docs/01-user-guide/03-open-six-frame-display/display_types_track_menu.png b/...bsite/docs/01-user-guide/03-open-six-frame-display/display_types_track_menu.png
diff --git a/packages/website/docs/01-user-guide/03-open-six-frame-display/index.md b/packages/website/docs/01-user-guide/03-open-six-frame-display/index.md
@@ -1,10 +1,29 @@
 # Open six-frame display
 
+Open the Apollo track's six-frame display mode.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
-are local and not shared, so no need to worry about affecting the annotations
-anyone else using this guide sees.
+where you can try out the steps for yourself. ANAny annotations you create or
+edit are local and not shared, so no need to worry about affecting the
+annotations anyone else using this guide sees.
 
 :::
+
+<a href="/demo//?assembly=Onchocerca%20volvulus&loc=OVOC_OM2:7815701-7818501&tracks=onchocerca_volvulus.PRJEB513.WBPS19.genomic-ReferenceSequenceTrack,apollo_track_Onchocerca%20volvulus&apolloFeatures=H4sIAAAAAAAAA82YyW7bMBBAf6WYs1qQWihKtyYFemodNEVzMAKBpKiEgEU5lJwmCPzvBe2k8VKKlaWDT4YxQ82DZ_RI-gVmWtw3QhrBPjw2i8fVYtVCPn-BQpWQA2GR5GFJ40jEPKtiVJYo5BhDAEZW1_IBcpj9ml0Ws28hBNA9LyXkcCe1hABqpSFPKU5STAKo2dPmG41TEkDbGaZLyD_iAMS9WpRGashfHAVRbGN9SCjuR6p_fP88JRKrSg-SzehFkk-NdiIlFMX7SKzrjOKrTra28F1VFW2zMkJCPoebxtQXrJVwu14HLhzpBZbDgLMEvQMTROnEwJUXuBoETEKKd4CjLJsUmCPknVI0DDhNd0aCZCSZGBh7gT1v-gFwimj0DpyG4bQzzFHoBQ4HAdOo3wOjgSMvcNQPfPnleoC3_o832EQs1Nw-P7dVcZTgmL3FNKs3a_YjSyNLJTrV6KLtWLfZKeCKmU6xxeK5EI2ulKllaXN_N6ZeyuX2IVc4JojaH2p9CuNPw3QrjFp2O6ifsBt2G3MgOHvFvb3iwzYZmu00K40QGrzvJV6kZJiz95AmdzZHxAtMzsvZqRc4PS9nUy8wHePsoykdDZx5gbNBCsziCXidCuROq3CnAi_7xJfQeFLx8R7x8X-L7xXB1SHsPbdgz7nlUHx7LSI0HS4-4R0aMfCwuoc0vfh81wGbcVbi810HbMYI8R01fTSw7zpgM072yKm8To8I50sqTvMIwcmkHhE9HhGOA9QIhK9Sy_zmwn4gFCYJQdFh-eNoKx9WUgt5TGijXDXbzs5haZpOKl2IplT6brO0KTpp6r8r9zOKzV8UtwGIlVGvxR10bKFYe1B7vb5d_wGcPevXOxEAAA"
+className="button button--primary button--lg" target="\_blank">Try
+it out</a>
+
+---
+
+From the Apollo track menu, under the "Display types" category choose
+"LinearApolloSixFrameDisplay."
+
+![Display types in track menu](display_types_track_menu.png)
+
+The six-frame view allows a different way of inpsecing the coding sequences of
+annotations. To switch back to the original display, choose
+"LinearApolloDisplay" in the "Display types" menu category.
+
+![Six frame display](six_frame_display.png)
diff --git a/...ages/website/docs/01-user-guide/03-open-six-frame-display/six_frame_display.png b/...ages/website/docs/01-user-guide/03-open-six-frame-display/six_frame_display.png
diff --git a/...site/docs/01-user-guide/04-add-gene-from-rna-seq/add_coding_sequence_dialog.png b/...site/docs/01-user-guide/04-add-gene-from-rna-seq/add_coding_sequence_dialog.png
diff --git a/...ite/docs/01-user-guide/04-add-gene-from-rna-seq/alignment_read_context_menu.png b/...ite/docs/01-user-guide/04-add-gene-from-rna-seq/alignment_read_context_menu.png
diff --git a/packages/website/docs/01-user-guide/04-add-gene-from-rna-seq/cds_added.png b/packages/website/docs/01-user-guide/04-add-gene-from-rna-seq/cds_added.png
diff --git a/...ebsite/docs/01-user-guide/04-add-gene-from-rna-seq/create_annotation_dialog.png b/...ebsite/docs/01-user-guide/04-add-gene-from-rna-seq/create_annotation_dialog.png
diff --git a/packages/website/docs/01-user-guide/04-add-gene-from-rna-seq/index.md b/packages/website/docs/01-user-guide/04-add-gene-from-rna-seq/index.md
@@ -1,10 +1,43 @@
 # Add gene from RNA-seq
 
+Add a gene from an JBrowse alignments track RNA-seq read.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 
 :::
+
+<a href="/demo//?assembly=Trichuris%20trichiura&loc=TTRE_chr2:19010000..19,012,000&tracks=Trichuris trichiura-ReferenceSequenceTrack,apollo_track_Trichuris%20trichiura,TTRE_all_isoseq.chr2&tracklist=true"
+className="button button--primary button--lg" target="\_blank">Try
+it out</a>
+
+---
+
+In this JBrowse evidence track, we have RNA-seq reads that show evidence for a
+gene in this location. To add a gene annotation from this evidence, right-click
+on one of the reads in the evidence track and click "Create Apollo annotation."
+
+![Alignment read context menu](alignment_read_context_menu.png)
+
+In the dialog that appears, select "Create".
+
+![Create annotation dialog](create_annotation_dialog.png)
+
+Now we have a gene with one transcript in our annotations. We probably also want
+to add a coding sequence to this transcript. To do so, right-click on the
+transcript and choose "Add coding sequence" from the mRNA sub-menu.
+
+![Transcript menu](transcript_menu.png)
+
+In the dialog that appears, select "Submit".
+
+![Add coding sequence dialog](add_coding_sequence_dialog.png)
+
+You can now see that a coding sequence has been created for this transcript
+using the longest open reading frame.
+
+![CDS has been added](cds_added.png)
diff --git a/packages/website/docs/01-user-guide/04-add-gene-from-rna-seq/transcript_menu.png b/packages/website/docs/01-user-guide/04-add-gene-from-rna-seq/transcript_menu.png
diff --git a/packages/website/docs/01-user-guide/05-merge-genes/index.md b/packages/website/docs/01-user-guide/05-merge-genes/index.md
@@ -1,9 +1,11 @@
 # Merge genes
 
+Merge two gene annotations into a single one.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 

diff --git a/packages/website/docs/01-user-guide/06-duplicate-a-transcript/index.md b/packages/website/docs/01-user-guide/06-duplicate-a-transcript/index.md
@@ -1,9 +1,11 @@
 # Duplicate a transcript
 
+Duplicate an existing transcript within a gene annotation.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 

diff --git a/packages/website/docs/01-user-guide/07-merge-transcripts/index.md b/packages/website/docs/01-user-guide/07-merge-transcripts/index.md
@@ -1,9 +1,11 @@
 # Merge transcripts
 
+Merge two transcripts into a single one.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 

diff --git a/packages/website/docs/01-user-guide/08-modify-exon-coordinates/index.md b/packages/website/docs/01-user-guide/08-modify-exon-coordinates/index.md
@@ -1,9 +1,11 @@
 # Modify an exon's coordinates
 
+A few different ways to modify the coordinates of an exon.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 

diff --git a/packages/website/docs/01-user-guide/09-add-exon-to-transcript/index.md b/packages/website/docs/01-user-guide/09-add-exon-to-transcript/index.md
@@ -1,9 +1,11 @@
 # Add an exon to a transcript
 
+Add a new exon to an existing transcript.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 

diff --git a/packages/website/docs/01-user-guide/10-merge-exons/index.md b/packages/website/docs/01-user-guide/10-merge-exons/index.md
@@ -1,9 +1,11 @@
 # Merge exons
 
+Merge two existing exons in a transcript.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 

diff --git a/packages/website/docs/01-user-guide/11-delete-an-exon/index.md b/packages/website/docs/01-user-guide/11-delete-an-exon/index.md
@@ -1,9 +1,11 @@
 # Delete an exon
 
+Delete an exon in a transcript.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 

diff --git a/packages/website/docs/01-user-guide/12-add-an-intron/index.md b/packages/website/docs/01-user-guide/12-add-an-intron/index.md
@@ -1,9 +1,11 @@
 # Add An Intron
 
+Add an intron to an existing exon.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 

diff --git a/packages/website/docs/01-user-guide/13-add-feature-from-region/index.md b/packages/website/docs/01-user-guide/13-add-feature-from-region/index.md
@@ -1,9 +1,11 @@
 # Add a feature from a region
 
+Add a new annotation by selecting a region for its boundaries.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 

diff --git a/packages/website/docs/01-user-guide/14-flip-strand/index.md b/packages/website/docs/01-user-guide/14-flip-strand/index.md
@@ -1,9 +1,11 @@
 # Flip strand
 
+Change the strand of a feature between forward and reverse.
+
 :::tip
 
 Every page in this guide has a "Try it out" button. This will take you to a page
-where you can try out the steps for yourself. ANy annotations you create or edit
+where you can try out the steps for yourself. Any annotations you create or edit
 are local and not shared, so no need to worry about affecting the annotations
 anyone else using this guide sees.
 

diff --git a/packages/website/docusaurus.config.ts b/packages/website/docusaurus.config.ts
@@ -21,7 +21,6 @@ const config: Config = {
   projectName: 'Apollo3', // Usually your repo name.
 
   onBrokenLinks: 'throw',
-  onBrokenMarkdownLinks: 'warn',
 
   trailingSlash: false,
 
@@ -33,6 +32,12 @@ const config: Config = {
     locales: ['en'],
   },
 
+  markdown: {
+    hooks: {
+      onBrokenMarkdownLinks: 'warn',
+    },
+  },
+
   presets: [
     [
       'classic',

diff --git a/packages/website/package.json b/packages/website/package.json
@@ -13,20 +13,20 @@
     "write-translations": "docusaurus write-translations"
   },
   "dependencies": {
-    "@docusaurus/core": "3.5.2",
-    "@docusaurus/preset-classic": "3.5.2",
-    "@docusaurus/remark-plugin-npm2yarn": "^3.6.3",
+    "@docusaurus/core": "^3.10.1",
+    "@docusaurus/preset-classic": "^3.10.1",
+    "@docusaurus/remark-plugin-npm2yarn": "^3.10.1",
     "@mdx-js/react": "^3.0.0",
     "clsx": "^1.1.1",
     "prism-react-renderer": "^2.3.0",
     "react": "^18.2.0",
     "react-dom": "^18.2.0"
   },
   "devDependencies": {
-    "@docusaurus/module-type-aliases": "^3.5.2",
-    "@docusaurus/theme-classic": "^3.5.2",
-    "@docusaurus/tsconfig": "^3.5.2",
-    "@docusaurus/types": "^3.5.2",
+    "@docusaurus/module-type-aliases": "^3.10.1",
+    "@docusaurus/theme-classic": "^3.10.1",
+    "@docusaurus/tsconfig": "^3.10.1",
+    "@docusaurus/types": "^3.10.1",
     "@types/node": "^24.10.9",
     "@types/react": "^18.3.4",
     "typescript": "^5.5.3"