# Data preparation

To run OptiMAS v1.5, you must supply data containing all information about your MAS design, i.e. genotype/pedigree data, a classic genetic map, and information on QTLs. Quantitative traits and allelic effects also can be supplied optionally.

Four input files are needed: a genotypes/pedigree file (containing also possibly quantitative traits), a classic map file with marker positions, a QTL positions file, and a file used to assign a list of marker to each QTL). An additional optional one for allelic effects can also be provided. Examples of these files (blanc.dat, blanc.map, blanc.qtlpos, blanc.qtll, and allelic_effects_blanc.txt) are supplied within the user’s home directory [/user_name/OptiMAS/input/] for multiparental designs. Note that all these files must be in plain-text, tab-delimited format and that the markers present in the map file must be ordered. To analyze your own data, you must prepare the input files in the appropriate format (as described below). Note that OptiMAS does not check that your input files are strictly conform to their expected format. This may lead to errors not necessarily detectable by the software.