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mcscanx website  

MCScan is an algorithm to scan multiple genomes or subgenomes to identify putative homologous chromosomal regions, then align these regions using genes as anchors. MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity and extends the software by incorporating 15 utility programs for display and further analyses.

Environment Modules

Run module spider mcscanx to find out what environment modules are available for this application.

System Variables

  • HPC_MCSCANX_DIR - installation directory
  • HPC_MCSCANX_BIN - executable directory
  • HPC_MCSCANX_INC - include directory
  • HPC_MCSCANX_DAT - data directory


If you publish research that uses mcscanx you have to cite it as follows:

Wang Y, Tang H, DeBarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH. (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res, 40(7): e49.