ABSTRACT
This chapter focuses on computer software for marker analysis, linkage map construction and quantitative trait locus (QTL) mapping. It discusses some problems with the available software packages and the future direction of the development of computer software for genomics. The chapter introduces the software package plant genome research initiative (PGRI). Compared to the general statistical analyses of biological data, the statistical analyses for the study of genes controlling complex traits have the following characteristics: many repeated analyses in one task, lack of standard distributions for some test statistics, and same level of complexity as models used in QTL mapping. Most of the available models for QTL mapping can be implemented using statistical software packages such as SAS. The analytical tools include gel reading devices, data quality control software, genetic analysis software and computational tools for the application of genomic information.
