MCScanX is a toolkit for detecting and visualizing synteny blocks between plant genomes. It extends MCScan by detecting collinearity across multiple genomes simultaneously, identifying whole genome duplication (WGD) events, and classifying gene pairs into different duplication types.

How do I run MCScanX online?

Upload your plant genome BED and PEP (protein) files on the PGDD pipeline page, select 2 or more genomes, configure parameters, and click Run Analysis. Results include collinearity blocks, dotplots, and Ka/Ks values — no software installation required.

What file formats does the MCScanX pipeline accept?

The pipeline accepts BED files (gene coordinates), FASTA protein files (PEP), and optionally CDS FASTA files. You can also upload raw genome assemblies (FASTA + GFF3) and let PGDD convert them automatically, or import directly from NCBI RefSeq or Phytozome.

What is whole genome duplication (WGD) in plants?

Whole genome duplication (WGD), also called polyploidy, is an evolutionary event where an organism's entire genome is duplicated. Plants have undergone multiple rounds of WGD throughout evolution. MCScanX can detect these ancient duplication events by identifying syntenic gene pairs in collinearity blocks.

Can I import genomes from NCBI or Phytozome?

Yes. PGDD integrates directly with NCBI RefSeq and JGI Phytozome. Search by species name or accession number, select an assembly, and PGDD will automatically download and process it — no manual file handling required.

MCScanX Online Pipeline – Run Synteny & WGD Analysis Free

Step 1 · Upload Your Genome Optional

Skip this step if you only want to use PGDD genomes — your uploaded genome will appear in "My Uploads" on the next step.

Species Name

Abbreviation

Gene Coordinates (BED/GFF)

Drop .bed / .gff here or click chr gene start end

Protein Sequences * (PEP/FAA – required)

Drop .pep / .faa here or click FASTA protein sequences

CDS Sequences (optional — needed for Ka/Ks)

Drop .cds / .fna here or click Coding nucleotide sequences

Species Photo (optional — JPG/PNG)

Drop .jpg / .png here or click Thumbnail shown in galleries

Data Source

Where the genome data comes from

Geographic Origin

Collection site or geographic region

Strain

Strain designation if applicable

Cultivar

Cultivar name if applicable

Sequencing Technology

Platform used for sequencing

Genome Version

Assembly or release version

Publication Reference

DOI, URL, or citation

Notes

Make genome public

Notify when analysis completes (optional)

Species Name

Abbreviation

Genome Assembly * (.fa, .fasta, .fa.gz)

Drop genome FASTA here or click Plain or gzip compressed

GFF3 Annotation * (.gff3, .gff, .gff.gz)

Drop GFF3 annotation here or click Gene + CDS features required

Codon Table (default: Standard)

Species Photo (optional)

Drop image here or click

Processing steps: Parse GFF3 → extract CDS → translate to protein → generate BED coordinates. Large genomes (>500 MB) may take 5–15 minutes. You'll be notified on completion.

Data Source

Where the genome data comes from

Geographic Origin

Collection site or geographic region

Strain

Strain designation if applicable

Cultivar

Cultivar name if applicable

Sequencing Technology

Platform used for sequencing

Genome Version

Assembly or release version

Publication Reference

DOI, URL, or citation

Notes

Make genome public

Step 3 · Configure Parameters

Search Parameters

BLAST E-value

Significance threshold for homolog detection.

Min Anchors (MCScanX)

Minimum collinear gene pairs per block.

Max Gap (MCScanX)

Max intervening genes allowed in a block.

Synteny Analysis Tool

Select Tool

MCScanX is recommended for most analyses. JCVI MCScan generates a karyotype/ribbon plot with Ks analysis.

Protein Similarity Search

Search Tool

MMseqs2 is recommended for speed when running MCScanX. JCVI MCScan uses LAST natively.

Visualization Options

Open Microsynteny Browser after completion

Opens the local gene-level synteny browser when results are ready.

Open SynVisio / MultiSynteny after completion

Opens the interactive synteny block viewer when results are ready.

Substitution Rate Analysis (Ka/Ks)

Calculate Ka/Ks (requires CDS for all genomes) Estimates synonymous/non-synonymous substitution rates

⚠️ Note: Ka/Ks analysis requires CDS files for ALL selected genomes. If any genome lacks CDS, this analysis will be skipped.

Calculation Method

Max Gene Pairs

Pairs sampled if total exceeds this.

Duplicate-Gene Classifier

Outgroup species (used for transposed-duplicate detection)

Auto-picks one of the other selected species. Leave blank unless you have a preferred outgroup.

Per-duptype Ka/Ks + GMM (Scripts_for_GB)

Runs Ka/Ks separately for each duplicate type (WGD, tandem, proximal, transposed, dispersed) with GMM peak detection per duptype. Requires CDS files.

Max pairs per duptype

Ortholog Detection (OrthoFinder)

Run OrthoFinder analysis Identify orthologs, paralogs, and in-paralogs

ℹ️ OrthoFinder uses BLAST results to infer ortholog relationships. Results include Venn diagram, GO enrichment, and CAFE analysis.

Block Filtering (Quota-Align) MCScanX only

Filter blocks using quota-align Retain only specified orthology ratios

ℹ️ Quota-align filters synteny blocks to show only specified orthology quotas (e.g., 1:1 orthologs only).

MCScanX Pipeline

Selected Assembly

Selected Organism

Selected Assembly

Detected Files

Selected Assembly

Selected Assembly

Search Parameters

Synteny Analysis Tool

Protein Similarity Search

Visualization Options

Substitution Rate Analysis (Ka/Ks)

Duplicate-Gene Classifier

Ortholog Detection (OrthoFinder)

Block Filtering (Quota-Align) MCScanX only

Analysis Complete!