MCScan 0.8 / MCScanX / MCScanX-transposed – Scan multiple Genomes to Identify Homologous Chromosomal Regions and more

MCScan 0.8 / MCScanX/ MCScanX-transposed


MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently 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.

MCScanX-transposed: detecting transposed gene duplications based on multiple collinearity scans


Haibao Tang : bao at uga dot edu and  Yupeng Wang: at Plant Genome Mapping Laboratory, University of Georgia




  • Linux /MacOsX
  • Java


 MCScan  / MCScanX / MCScanX-transposed



Bioinformatics. 2013 Jun 1;29(11):1458-60. doi: 10.1093/bioinformatics/btt150. Epub 2013 Mar 28.
MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans.
Wang Y1, Li J, Paterson AH.

Nucleic Acids Res. 2012 Apr;40(7):e49. doi: 10.1093/nar/gkr1293. Epub 2012 Jan 4.
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.
Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH.