QGENE: Software for marker-based genomic analysis and breeding

Efficient use of DNA markers for genomic research and crop improvement will depend as much on computational tools as on laboratory technology. The large size and multidimensional character of marker datasets invite novel approaches to data visualization. Described here is a software application embodying two design principles: conventional reduction of raw genetic marker data to numerical summary statistics, and fast, interactive graphical display of both data and statistics. The program performs various analyses for mapping quantitative-trait loci in real or simulated datasets and other analyses in aid of phenotypic and marker-assisted breeding. Functionality is described and some output is illustrated.