MapMaker

MapMaker is a set of applications that can be used in order to build genetic linkage maps and performing gene mapping.
Delivered inside a lightweight package, it bundles two command line tools, namely MAPMAKER/EXP and MAPMAKER/QTL. The first one comes with options for generating the primary linkage groups and analyzing the output to determine the dominant, co-dominant and recessive markers, whereas the latter helps you map genes by making use of the previously generated linkage maps.
MAPMAKER/EXP works with flat ASCII text files that contain the data set derived from various types of crosses (backcross, intercross, testcross, haploid data). The other application only works with F2 intercross and backcross data.
You start by preparing the data set for analysis and load it in MAPMAKER/EXP. The application comes with a wide range of commands that you can use to list, edit, name or erase genetic sequences, insert markers within a sequence.
You can use it to perform pairwise analysis for pairs of markers and conduct multi-point analysis. It can assign markers to a chromosome and display the mapping status of Some Loci.
The program features genotyping error detection capabilities and enables you to join haplotypes together into a single data set. It can save the data to a database and save the status and the mapping results to your computer.
MAPMAKER/QTL is used for gene mapping, featuring various trait commands and enabling you to save the obtained data in PostScript, compare QTL maps and so on.