The MCScanX package has two major components: a modified version of MCscan algorithm allowing users to handle MCScan more conveniently and to view multiple alignment of syntenic blocks more clearly, and a variety of downstream analysis tools to conduct different biological analyses based on the synteny data generated by the modified MCScan algorithm.

For more information, please check:


  • default


  • MCScanX

  • MCScanX_h

  • duplicate_gene_classifier

  • add_ka_and_ks_to_collinearity

  • add_kaks_to_synteny

  • detect_collinearity_within_gene_families

  • detect_synteny_within_gene_families

  • group_collinear_genes

  • group_syntenic_genes

  • origin_enrichment_analysis


You can load the modules by:

module load biocontainers
module load mcscanx

Helper command


To conduct downstream analyses, users need to copy the folder downstream_analyses from container into the host system.

A helper command copy_downstream_analyses is provided to simplify the task. Follow the procedure below to copy downstream_analyses into target directory:

$ copy_downstream_analyses $PWD # this will copy the downstream_analyses into the current directory.

Example job


Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run mcscanx on our clusters:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -n 1
#SBATCH --job-name=mcscanx
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers mcscanx

## Run MCScanX
MCScanX Result/merge
## Copy downstream_analyses
copy_downstream_analyses $PWD
## Downstream analyses
java circle_plotter -g ../Result/merge.gff -s ../Result/merge.collinearity -c ../Result/merge_circ.ctl -o ../Result/merge_circle.png
java dot_plotter -g ../Result/merge.gff -s ../Result/merge.collinearity -c ../Result/merge_dot.ctl -o ../Result/merge_dot.png
java dual_synteny_plotter -g ../Result/merge.gff -s ../Result/merge.collinearity -c ../Result/merge_dot.ctl -o ../Result/merge_dual_synteny.png