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MCScanX specifications


Unique identifier OMICS_11717
Name MCScanX
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Xcode, JDK, libpng
Maintained Yes


No version available



  • person_outline Yupeng Wang

Publication for MCScanX

MCScanX citations


Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species

BMC Genomics
PMCID: 5944053
PMID: 29743014
DOI: 10.1186/s12864-018-4744-4

[…] contributed the most to the expansion of this gene family in many plant lineages. We examined 5 types of gene duplications: singleton, dispersed, proximal, tandem, and WGD or segmental duplication by MCScanX program (Table , Additional file : Table S3). The percentage of WGD was 75.0% in B. napus, B. rapa (80.0%), B. oleracea (84.6%), and A. thaliana (62.5%) (Table ). However, WGD or segmental dup […]


Genome wide analysis of GRAS transcription factor gene family in Gossypium hirsutum L.

BMC Genomics
PMCID: 5944045
PMID: 29743013
DOI: 10.1186/s12864-018-4722-x

[…] each chromosome was calculated using a Perl script. Then, we made a diagram of the GRAS members that showed duplications among 26 chromosomes and identified five types of gene duplication events with MCScanX using the GRAS protein sequences and the position data in chromosomes []. Additionally, we made a diagram of the chromosomal locations with the MapInspect software []. […]


Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] ts (Supplementary File : Table S7) using MEGA v6.0 with the maximum-liklihood algorithm (Tamura et al., ).Syntenic blocks between the genomes of A. ipaensis and other plants were identified using the MCScanX with default parameters (Wang et al., ) and visualized on the genome using Circos (Krzywinski et al., ). Genomic sequences were first aligned annotated genes based on amino acid sequence using […]


Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

PLoS Biol
PMCID: 5916493
PMID: 29689044
DOI: 10.1371/journal.pbio.2004830

[…] Syntenic regions within and between genomes were identified using MCScanX [], calling collinear ‘blocks’ regions with at least 5 homologous genes and fewer than 10 ‘gaps’ (i.e., missing genes). Rates of synonymous (KS) and nonsynonymous (KA) substitution between pai […]


The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

Nat Commun
PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] A homolog search within the G. elata genome was performed using BLASTP (E-value < 1e−7), and MCscanX was used to identify syntenic blocks within the genome. For each gene pair in a syntenic block, the 4DTv (transversion substitutions at fourfold degenerate sites) distance was calculated, and […]


Genome Wide Identification, Evolutionary, and Expression Analysis of VQ Genes from Two Pyrus Species

PMCID: 5924566
PMID: 29690608
DOI: 10.3390/genes9040224

[…] tions and genome evolution among species. To gain insight into the evolution of P. bretschneideri and P. communis VQ motif-containing genes, the syntenic blocks were searched in the chromosomes using MCScanX software. Among them, 31 orthologous pairs were identified within these pairwise syntenic blocks ( and ). Additionally, we also observed a reciprocal homology in syntenic blocks between the P. […]

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MCScanX institution(s)
Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, University of Georgia, Athens, GA, USA; Department of Plant Biology, University of Georgia, Athens, GA, USA; J. Craig Venter Institute, Chinakville, MD, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA; Center for Genomics and Computational Biology, School of Life Sciences and School of Sciences, Hebei United University, Tangshan, Hebei, China; Department of Genetics and 8Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
MCScanX funding source(s)
National Science Foundation (NSF: DBI 0849896, MCB 0821096, MCB 1021718); National Institutes of Health (R01 AI068908) in part; resources and technical expertise from the University of Georgia, Georgia Advanced Computing Resource Center in part

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