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| Name and link | Description |
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| MetaQTL http://bioinformatics.org/mqtl/ | A java package designed to perform the integration of data from the field for gene mapping experiments |
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| BioMercator http://cms.moulon.inra.fr/index.php?option=com_content&task=view&id=13&Itemid=43 | Genetic maps and QTL integration |
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| CMTV http://www.ncgr.org/cmtv/ | An integrated bioinformatics tool to construct consensus maps and compare QTL and functional genomics data across genomes and experiments |
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| QTL-Finder http://gqtl.maizecenter.cn | A bioinformatics tool for QTL integration, comparison and candidate gene discovery across genomes and experiments |
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| TWINSCAN http://mblab.wustl.edu/query.html | Improved gene prediction performance for maize and rice |
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| GDPC http://www.maizegenetics.net/gdpc/index.html | The genomic diversity and phenotype connection (GDPC) simplifies access to genomic diversity and phenotype data, thereby encouraging reuse of this data. GDPC accomplishes this by retrieving data from one or more data sources and by allowing researchers to analyze integrated data in a standard format. GDPC provides access to genomic diversity data such as SNPs, SSRs, and sequences, and phenotypic data that may be collected in field, genetic, or physiological experiments |
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| TASSEL http://www.maizegenetics.net/index.php?page=bioinformatics/tassel/index.html | A software package to evaluate trait associations, evolutionary patterns, and linkage disequilibrium |
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| PowerMarker http://statgen.ncsu.edu/powermarker/ | A comprehensive set of statistical methods for genetic marker data analysis, designed especially for SSR/SNP data |
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| RepMiner http://jestill.myweb.uga.edu/RepMiner.htm | Takes a graph theory approach to the identification and assembly of transposable elements from small DNA fragments resulting from subcloning bacterial artificial chromosome libraries |
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| SPAGeDi http://www.ulb.ac.be/sciences/ecoevol/spagedi.html | Spatial Pattern Analysis of Genetic Diversity (SPAGeDi) is a new computer package—replacing AutocorG that was distributed to a limited extent—primarily designed to characterize the spatial genetic structure of mapped individuals and/or mapped populations using genotype data of any ploidy level |
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| Structure http://pritch.bsd.uchicago.edu/structure.html | A free software package for using multilocus genotype data to investigate population structure |
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| TEnest http://bak.public.iastate.edu/te_nest.html | Automated chronological annotation and visualization of maize nested transposable elements |
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