MCScanX 2016

Introduction

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

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]
 -k  MATCH_SCORE, final score=MATCH_SCORE+NUM_GAPS*GAP_PENALTY
     (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

Documentation

The full documentation can be found here.