Tutorials
Step-by-step guides for using PGDD tools
Video tutorials are coming soon!
We are preparing video walkthroughs for each feature below.
Check back shortly or request a specific tutorial.
Coming Soon
Comparative Synteny Analysis with Two Plant Genomes
Learn how to compare two plant genomes using the MCScanX pipeline: upload files, set parameters, and interpret synteny blocks.
- Upload protein FASTA and GFF files
- Configure search and synteny tools
- Explore results in SynVisio and Chromosome Browser
Coming Soon
Multi-Genome Karyotype with JCVI MCScan
Use JCVI MCScan to generate a chromosome-scale karyotype plot across 3+ genomes.
- Prepare multi-genome inputs
- Select JCVI MCScan in the pipeline
- Download and interpret the karyotype PDF
Coming Soon
Ka/Ks Analysis for Detecting Selection
Calculate synonymous and non-synonymous substitution rates to identify genes under selection.
- Provide CDS FASTA files
- Enable Ka/Ks in pipeline settings
- Interpret Ks distribution plots
Coming Soon
Gene Locus Search and Syntenic Orthologs
Search for a gene and explore its syntenic orthologs across genomes.
- Use the Locus Search page
- Navigate the locus detail view
- Export syntenic gene pairs
Coming Soon
Uploading a Custom Genome for Analysis
Add your own genome data for private or public synteny analysis.
- Register/login to PGDD
- Upload genome files via the pipeline page
- Share results publicly or keep private
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