# Running OptiMAS Graphical User Interface (GUI)

To run the program, you must specify the paths to the genetic map file and the genotypes/pedigree file (see previous sections). Select File > Import Data... from the menu bar (see below).

Figure 5: data set importation to run the program

Loading input/output files using the browser:

Map file: path to the genetic map input file (.map).
Remarks: QTLs information files and map file has to be in the same folder, and share the same base name, e.g. blanc.map blanc.qtlpos and blanc.qtll. Note that the method used to determine markers flanking the QTL is determined by the file(s) found in the same folder. If several files describing markers to be used to track QTL are present in the directory, only one will be used, according to priority rule .qtll > .qtln > .qtlw.
Genotype file: path to the genotype/pedigree file (.dat).
Allelic effects file (optional, can be loaded/refreshed after loading mandatory files): path to the allelic effects file. May be located in any folder.
See allelic effects section for more details on its structure.
Output directory: path to the folder where the results will be stored. Results from each run will be stored within a new dated directory created automatically within this folder. Note that your output directory should not be in the "Program Files" folder or other specific directories with administrator privileges.

Advanced options/parameters:

QTL analyzed: by default all the QTL present in the input files will be analyzed. You can also choose to select a specific QTL to run the analysis.
Cut-off - Diplotypes: genotypic probability below which a rare phased genotype (diplotype) is removed and no more considered in subsequent computations (default value = 0.000001).
Cut-off - Gametes: (default value = 0.000000). It corresponds to the probability that the number of crossovers expected in the region between flanking markers exceeds a given value. Thus, unlikely gametes with number of crossovers over this value are removed and no more considered in subsequent computations. Use of this option with values up to 0.01 is recommended in case many flanking markers per QTL lead to high computation time with default option.
Verbose: Verbose mode creates two files per QTL position, reporting respectively gamete and diplotype probabilities for all individuals (default value = ON).
WARNING: With large/complex data, both files may take a lot of disk space, it is then recommended to disable this option.

Click on the "Run" button to analyze the data set. The program will create output results in the folder that you specified. At the end of the run (the progress bar displays 100%), close the "Import data..." window by pressing the "Close" button. If a warning message appears report to section Results & Output files and Tools to analyze these questionable results before any interpretation.

Note: it is also possible to directly display the results of previous analyses by selecting File > Reload data. You can also display results from the two examples data sets provided with the program, that are located in File > Example Data > Biparental or Multiparental from the menu bar.

To visualize and analyze the results, the OptiMAS GUI includes three modules (on the left menu) corresponding to the different steps of the selection programme (see below).

To show and use the full functionalities of OptiMAS, this analysis will focus on real data coming from a multiparental marker-assisted recurrent selection (MARS) study (Blanc et al., 2006, 2008).

Six connected F2 populations, with 150 individuals each, were obtained from a half-diallel design between four unrelated maize inbred lines (DE, F283, F810 and F9005). Eleven QTL were detected for silking date. A set of 34 markers was selected with at least three markers (microsatellites) to follow each QTL (see blanc.map & blanc.dat files). Two cycles of MARS were performed with each time a step of selfing before intermating. In this example, OptiMAS is used at the last cycle to select the best individuals (among 297 genotyped plants) that will be used for the next cycle of MARS (see below).

Figure 6: multiparental MAS study (Blanc et al., 2006, 2008) used as example within OptiMAS

To run the multiparental example data set, you must supply four input files (blanc.dat, blanc.map, blanc.qtlpos & blanc.qtll, see previous sections) or it is also possible to directly display the results of this previous analysis from the menu bar (i.e. File > Example Data > Multiparental).