MCScanX 2016

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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. 1

The original software package, MCscan itself, provides a clustering module for viewing the relationship of colinear segments in multiple genomes (or heavily redundant genomes). It takes the predicted pairwise segments from dynamic programming (DAGchainer in particular) and then try to build consensus segments from a set of related, overlapping segments. 1

Installed version(s)

The following versions are installed and currently available...

... on environment hpc-env/8.3:

  • MCScanX/10.2020-GCCcore-8.3.0

Since MCScanX is not versioned at the software repository our HPC team generated the version number, and it represents the last change made on GitHub (<month>.<year>).

Loading / Using MCScanX

To load the desired version of the module, use the module load command, e.g.

module load hpc-env/8.3
module load MCScanX

Always remember: this command is case sensitive!

MCScanX includes a lot of scripts and some executables which you can print out by this command: ls -l $EBROOTMCSCANX/bin after loading the module. To find out on how to use the MCScanX executable you can just type in MCScanX -h to print out a help text to get you started:

$ MCScanX -h
[Usage] MCScanX prefix_fn [options]
     (default: 50)
 -g  GAP_PENALTY, gap penalty (default: -1)
 -s  MATCH_SIZE, number of genes required to call a collinear block
     (default: 5)
 -e  E_VALUE, alignment significance (default: 1e-05)
 -m  MAX_GAPS, maximum gaps allowed (default: 25)
 -w  OVERLAP_WINDOW, maximum distance (# of genes) to collapse BLAST matches (default: 5)
 -a  only builds the pairwise blocks (.collinearity file)
 -b  patterns of collinear blocks. 0:intra- and inter-species (default); 1:intra-species; 2:inter-species
 -h  print this help page


The full documentation can be found here.