The Outcross Linkage Map Analyses add-in offers three processes to perform linkage analyses on a full-sib family derived from a cross of two outbred parents. The processes are the Linkage Group and Recombination, Linkage Map Order, and Build QTL Genotype Probability Data Set, and all of them run on an interface of JMP, SAS, and R. This add-in uses the OneMap (Margarido et al. 2007, Hereditas 144: 78-79) R package.
The newer release of JMP Genomics, version 7.1, has new features tailored to improve the capabilities of the software:
The Linkage Group and Recombination process has a new option to form linkage groups, the Transitive Grouping method, as well as a new option to set up R software memory usage.
The Linkage Map Order process has two new options to order markers, the Map Order Optimization and Accelerated Map Order Optimization. The former uses SAS PROC OPTMODEL, and the latter uses SAS PROC OPTNET, both of which are powerful and fast methods of optimization suitable to handle the ordering of many markers. Also, a new option to shuffle marker order is available, which may be used to improve overall ordering of markers by shuffling nearby markers on a linkage group.