MCScan is an algorithm able to scan multiple genomes or subgenomes in order to 
identify putative homologous chromosomal regions, and align these regions using 
genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm 
for detection of synteny and collinearity that extends the original software by 
incorporating 14 utility programs for visualization of results and additional 
downstream analyses. Applications of MCScanX to several sequenced plant genomes 
and gene families are shown as examples. MCScanX can be used to effectively 
analyze chromosome structural changes, and reveal the history of gene family 
expansions that might contribute to the adaptation of lineages and taxa. An 
integrated view of various modes of gene duplication can supplement the 
traditional gene tree analysis in specific families. The source code and 
documentation of MCScanX are freely available at 
http://chibba.pgml.uga.edu/mcscan2/.