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+Our grape vs peach dotplot demo has been useful for demonstrating our synteny
+capabilities
+
+### Pre-requisites
+
+- Install node.js (don't recommend installing from apt directly, try
+  nodesource's apt repository
+  https://github.com/nodesource/distributions#installation-instructions)
+- Install the JBrowse CLI tools `npm install -g @jbrowse/cli`, this should give
+  a command named `jbrowse` automatically in your PATH
+- Install minimap2 (`sudo apt install minimap2` or similar)
+- Install samtools (`sudo apt install samtools` or similar)
+
+## Run minimap2 to perform a whole genome alignment
+
+### Preparation for running minimap2
+
+Download the grape and peach genome assembly (FASTA) files from e.g. Phytozome
+(requires login)
+
+https://data.jgi.doe.gov/refine-download/phytozome?genome_id=457&expanded=Phytozome-457
+https://data.jgi.doe.gov/refine-download/phytozome?genome_id=298&expanded=Phytozome-298
+
+You can substitute your own FASTA files as needed for the purposes of the
+tutorial also
+
+### Run minimap2 to perform a whole genome alignment
+
+```bash
+minimap2 -c grape.fa peach.fa > peach_vs_grape.paf
+```
+
+The -c flag tells it to compute per-base alignment and output CIGAR strings to
+the PAF file. JBrowse will be fine if you don't specify -c, but the
+visualization will not show insertions and deletions within the alignment. Note
+that using -c will take longer to run also.
+
+The grape genome will be the "target" peach will by the "query"
+
+See also Footnote 1
+
+## Create FASTA indexes for the assemblies
+
+```bash
+samtools faidx grape.fa
+samtools faidx peach.fa
+```
+
+## Load the files into JBrowse
+
+Load the assemblies, this outputs to a folder in your "web directory" and says
+to copy the assemblies
+
+```bash
+jbrowse add-assembly grape.fa --load copy --name grape --out /var/www/html/jbrowse/
+jbrowse add-assembly peach.fa --load copy --name peach --out /var/www/html/jbrowse/
+```
+
+## Load the minimap2 synteny track
+
+```bash
+jbrowse add-track peach_vs_grape.paf --assemblyNames peach,grape --load copy --out /var/www/html/jbrowse
+```
+
+Note: Order matters here for the `--assemblyNames` parameter!
+
+If minimap2 is run as `minimap2 grape.fa peach.fa`, then you need to load as
+`--assemblyNames peach,grape`.
+
+The order is reversed between the `minimap2` and `jbrowse` tools. You can think
+of JBrowse as loading the "left column" of the PAF as the first in the
+--assemblyNames list, and the "right column" as the second name in the
+--assemblyNames list (the left column is query, and right is target)
+
+## Calculate synteny using MCScan (python version)
+
+### Intro
+
+The minimap2 method above does a whole-genome alignment. Configuring a whole
+genome alignment can be tricky and involved. Another method for computing
+synteny is to perform "all-vs-all BLASTP" e.g. aligning all protein sequences
+against each other to find homologous genes. The MCScan toolkit can perform this
+
+https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)
+
+### Preparation for running MCScan
+
+Download the grape and peach whole genome assembly FASTA files, e.g. from
+Phytozome (requires login)
+
+https://data.jgi.doe.gov/refine-download/phytozome?genome_id=457&expanded=Phytozome-457
+https://data.jgi.doe.gov/refine-download/phytozome?genome_id=298&expanded=Phytozome-298
+
+### Running MCScan
+
+```
+# Covert GFFs to bed files
+python -m jcvi.formats.gff bed --type=mRNA --key=Name Vvinifera_145_Genoscope.12X.gene.gff3.gz -o grape.bed
+python -m jcvi.formats.gff bed --type=mRNA --key=Name Ppersica_298_v2.1.gene.gff3.gz -o peach.bed
+```
+
+```
+# Format CDS sequences
+python -m jcvi.formats.fasta format Vvinifera_145_Genoscope.12X.cds.fa.gz grape.cds
+python -m jcvi.formats.fasta format Ppersica_298_v2.1.cds.fa.gz peach.cds
+
+```
+
+```
+# Run synteny calculations
+python -m jcvi.compara.catalog ortholog grape peach --no_strip_names
+```
+
+This final command will output .anchors (individual gene pairs) and
+.anchors.simple files (chained sets of genes forming a "syntenic block").
+JBrowse can load both these files as different tracks
+
+## Using JBrowse to visualize the dotplot
+
+After running the above steps, the configuration file will have the two
+assemblies and the SyntenyTrack(s) loaded. Open your web browser and navigate to
+http://yourhost/jbrowse/
+
+Select `Add->Dotplot view` from the main header bar
+
+Then select the "Grape" assembly for the first selector and "Peach" for the
+second from the "Import form". This will make Grape the X axis of the dotplot,
+and Peach the Y. You can also switch it if you want.
+
+Then, also select "Existing track" and which will give you a small select box
+asking what dataset/synteny track that you want to load into the Dotplot
+
+Then click Open, and the dotplot will be launched
+
+### Footnote 1 - whole genome alignment may require tweaking paramters
+
+Note properly performing a whole-genome alignment may require tweaking
+paramters, make sure to read the manual of e.g. minimap2 for more details
+
+### Footnote 2 - loading data from other tools
+
+Note that JBrowse 2 also supports loading data from other tools including MUMmer
+(.delta files), MashMap (.out files, similar to PAF but a little different), and
+UCSC liftover (.chain files). You can use these in place of the minimap2 step