Multiple Collinearity Scan - mcscan

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. This is the toolset for generating the synteny correspondences in Plant Genome Duplication Database. It is intended as an easy-to-use and quick way to identify conserved gene arrays both within the same genome and across different genomes.


Current production version: 0.8 (released Nov. 2008): GITHUB
Disclaimer: this software is free to use, modify, redistribute without any restrictions.
Installation: unpack the tarball and type "make" (Currently Linux and Cygwin platform are supported).
Documentation: PDF manual.

MCSCAN toolkit version: 1.1 (released Feb. 2016): MCSCAN-toolkit-beta-1.1.tgz
The MCSCAN toolkit is under development with the support of an NSF grant, aimed at deconvoluting the complex structures of plant genomes which have been subjected to rounds of genome duplication. This beta version of the toolkit is available for use and test. Suggestions are welcome. Xiyin Wang : wang dot xiyin at gmail dot com.
Installation: no installation is necessary. Simply decompress the downloaded files (~1.3G).
Documentation: find the included file "mcscan.docx".
Grass genome alignment data: grass8.ks.rar
Cotton-Cacao-Grape genome alignment data: Cotton-Cacao-Grape.alignment.tar


The MCscan algorithm has been tested in several taxonomic groups, including:

Results and procedures for plant species can be accessed here.



All bug reports, suggestions or questions are very welcome and should be dumped to

Haibao Tang : bao at uga dot edu

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