MAPMAKER Eric Lander's MAPMAKER program adapted by Russell Malmberg to run in a windows command prompt environment. try.py 'try.py' places markers in the position identified by the MAPMAKER 'try' command. When two markers map to the same interval, the marker with the biggest difference in likelihood between the most likely position and second-best position will be placed first. To place the second marker, a second round of MAPMAKER 'try' and 'try.py' needs to be run. Provide the MAPMAKER 'try' output as input (see 'lg1.txt' as example). The script generates an ordered sequence (see 'ordered_lg1.txt' as example) which can be used as input for MAPMAKER 'try'. Continue running until all markers are ordered. ripple_ver3.3.py 'ripple.try' uses MAPMAKER's 'ripple' command to check marker orders. If necessary, markers will be reordered, and this will be automatically followed by another round of 'ripple'. Reordering and rippling will continue until the most likely map order has been established. Provide the MAPMAKER raw data file (see 'mapmaker_lg1.txt' as example) and marker order (see 'ripple_order_lg1.txt' as example) as inputs. The final order will be found in the file that starts with 'Rippled'. 1_MST_to_Mapmaker.py If the total marker number is too high for mapmaker to handle, markers can be organized in linkage groups using MSTMap. The python script '1_MST_to_Mapmaker.py' uses the MSTmap output and mapmaker raw data file to generate individual mapmaker input data files for each linkage group. outcross-F1-AH-HA.py 'outcross-F1-AH-HA.py' prepares genotypic data obtained in an F1 population in a diploid outcrossing species for generation of maternal and paternal maps using MAPMAKER. Maternal maps consist of markers that are heterozygous in the maternal parent and homozygous in the paternal parent). Paternal maps consist of markers that are homozygous in the maternal parent and heterozygous in the paternal parent. Rescoring of markers is necessary to account for the fact that the linkage phase of markers is unknown (Qi et al., Scientific Reports, submitted). The input file (see 'AH_demo.txt as example) has to be (1) a tab delimited file; (2) The first row must comprise the sample names; (3) the First column must consist of the marker names and must have a header; (4) the original genotypic scores must have the values A/B/C/D/H/- with ‘A’ = homozygous parent 1; ‘B’ = homozygous parent 2; ‘C’ = homozygous parent 2 or heterozygous (ambiguous score); ‘D’ = homozygous parent 1 or heterozygous (ambiguous score); ‘H ’= heterozygous; ‘-‘ = missing data. outcross-F1-HH.py 'outcross-F1-HH.py' prepares genotypic data obtained in an F1 population in a diploid outcrossing species for generation of HH maps using MAPMAKER. HH maps consist of markers that are heterozygous in both parents. Rescoring of markers is necessary to account for the fact that the linkage phase of markers is unknown (Qi et al., Scientific Reports, submitted). See outcross-F1-AH-HA.py and example file HH_demo.txt for the format of the input file Example files lg1.txt ordered_lg1.txt mapmaker_lg1.txt ripple_order_lg1.txt AH_demo.txt HH_demo.txt
