the interface for the first set of data , pedigree relationships , is based on the concept of subpopulations . from the total population , various subpopulations can be selected and each can be viewed in different graphical presentations . these subpopulations can be assembled manually , but tools are available to automatically include or exclude further individuals based on their pedigree relations with another individual . in the simplest case , gapi_07  was selected , and all its ancestors and full sibs were added automatically using the tool for selection based on pedigree relationships . female parentage is indicated by pink ( light grey ) lines and male parentage by blue ( dark grey ) lines . the pedigree visualization forms the scaffold on which the next set of data , phenotypic data , is superimposed . qualitative phenotypic data can be color coded to reflect the different trait classes , whereas a color gradation can be used to represent variation for a quantitative trait ( figures 2 and 3 ) . screenshot of the user interface of pedimap with the subpopulations panel ( top left , with the  gapi selection  subpopulation selected ) , information panel ( bottom left , with information on the individual under the cursor ) , and the pedigree view ( right ) . the pedigree view shows the same subpopulation as figure 1 with apple crispness values indicated by color and with observed marker genotypes for 3 simple sequence repeat loci . in several cases individuals colored blue ( dark grey ) or pink ( light grey ) when resistant or susceptible to red root rot ( phytophthora fragariae ) , respectively . the octoploid genotypes at an ssr marker are shown ; the allele 145 ( in white ) is closely linked to the resistance gene ( data from a. pikunova et al . , wageningen ur - plant breeding ) . next to the pedigree and phenotypic data , genetic data ( observed marker genotypes ) can be added , organized by linkage group . the required information for each linkage group includes a linkage map : a list of locus names and map positions , and for each locus , the possible allele identifiers . the locus genotype of every individual is specified by 2 ( or more , in the case of polyploids ) allele identifiers . instead of an allele , a missing value or a symbol indicating a possible or a confirmed null allele can be given . it is possible to assign an allele a specific color , which can be useful to investigate the inheritance of specific alleles or to easily identify situations ( e.g. , contradictory genotypes ) that need further attention . the genetic data for selected marker loci can then be visualized along with the pedigree and phenotypic data ( figures 24 ) . a different part of the apple pedigree is shown with genotypes for 7 closely linked single nucleotide polymorphism ( snp ) markers ; the alleles per locus are listed in alphabetical order . snp haplotypes are reconstructed starting at the completely homozygous individual gala and shown in different colors ( snp data from dr michela troggio , istituto agrario di san michele alladige ) . these must be given in the input file as pedimap does not calculate these values itself . a package that can perform these calculations and produces output files compatible with pedimap is flexqtl ( bink et al . 2008 ; see also interfacing with other software ) . this visualization can help to follow the inheritance of a specific haplotype through the pedigree , even if several founders have the same marker allele at that position ( figure 5a ) . it can also illustrate how the founder chromosomes are progressively recombined through the generations ( figure 5b ; van dijk et al . 2012 ) . the same apple pedigree as in the first 3 figures is shown with precalculated ibd data for part of chromosome 1 . the color of the allele indicates the founder allele . a bold typeface indicates a high probability , normal and italic typefaces indicate lower probabilities according to user - specified thresholds . in panel b , again each color represents a different founder haplotype . each rectangle in an individual represents 1 of the 2 copies of the selected chromosome . the vertical dimension represents the positions along the chromosome ; the width of a color at a certain position indicates the ibd probability that the corresponding founder allele is present . pedimap is being used in several projects in close relation with flexqtl , software for qtl analysis and ibd calculations in multiple pedigreed populations ( bink et al . 2008 ) . in order to allow for easy exchange of data , both pedimap and flexqtl export data in the format required for the other program . in the case of pedimap , this involves the export of data from the complete pedigree or from selected subpopulations , and the filling - in of missing parents of  semi - founders  : individuals of which only 1 parent is known , which are accepted by pedimap but not by flexqtl . in order to import large amounts of snp data generated by illumina s genotyping platforms , a conversion script is available from the pedimap website that builds a data file in pedimap format from a text file exported by the genomestudio software ( http://www.illumina.com/software/ genomestudio_software.ilmn ) . the interface for the first set of data , pedigree relationships , is based on the concept of subpopulations . from the total population , various subpopulations can be selected and each can be viewed in different graphical presentations . these subpopulations can be assembled manually , but tools are available to automatically include or exclude further individuals based on their pedigree relations with another individual . in the simplest case , gapi_07  was selected , and all its ancestors and full sibs were added automatically using the tool for selection based on pedigree relationships . female parentage is indicated by pink ( light grey ) lines and male parentage by blue ( dark grey ) lines . the pedigree visualization forms the scaffold on which the next set of data , phenotypic data , is superimposed . qualitative phenotypic data can be color coded to reflect the different trait classes , whereas a color gradation can be used to represent variation for a quantitative trait ( figures 2 and 3 ) . screenshot of the user interface of pedimap with the subpopulations panel ( top left , with the  gapi selection  subpopulation selected ) , information panel ( bottom left , with information on the individual under the cursor ) , and the pedigree view ( right ) . the pedigree view shows the same subpopulation as figure 1 with apple crispness values indicated by color and with observed marker genotypes for 3 simple sequence repeat loci . in several cases individuals colored blue ( dark grey ) or pink ( light grey ) when resistant or susceptible to red root rot ( phytophthora fragariae ) , respectively . the octoploid genotypes at an ssr marker are shown ; the allele 145 ( in white ) is closely linked to the resistance gene ( data from a. pikunova et al . , wageningen ur - plant breeding ) . next to the pedigree and phenotypic data , genetic data ( observed marker genotypes ) can be added , organized by linkage group . the required information for each linkage group includes a linkage map : a list of locus names and map positions , and for each locus , the possible allele identifiers . the locus genotype of every individual is specified by 2 ( or more , in the case of polyploids ) allele identifiers . instead of an allele , a missing value or a symbol indicating a possible or a confirmed null allele can be given . it is possible to assign an allele a specific color , which can be useful to investigate the inheritance of specific alleles or to easily identify situations ( e.g. , contradictory genotypes ) that need further attention . the genetic data for selected marker loci can then be visualized along with the pedigree and phenotypic data ( figures 24 ) . a different part of the apple pedigree is shown with genotypes for 7 closely linked single nucleotide polymorphism ( snp ) markers ; the alleles per locus are listed in alphabetical order . snp haplotypes are reconstructed starting at the completely homozygous individual gala and shown in different colors ( snp data from dr michela troggio , istituto agrario di san michele alladige ) . these must be given in the input file as pedimap does not calculate these values itself . a package that can perform these calculations and produces output files compatible with pedimap is flexqtl ( bink et al . 2008 ; see also interfacing with other software ) . this visualization can help to follow the inheritance of a specific haplotype through the pedigree , even if several founders have the same marker allele at that position ( figure 5a ) . it can also illustrate how the founder chromosomes are progressively recombined through the generations ( figure 5b ; van dijk et al . the same apple pedigree as in the first 3 figures is shown with precalculated ibd data for part of chromosome 1 . a bold typeface indicates a high probability , normal and italic typefaces indicate lower probabilities according to user - specified thresholds . in panel b , again each color represents a different founder haplotype . each rectangle in an individual represents 1 of the 2 copies of the selected chromosome . the vertical dimension represents the positions along the chromosome ; the width of a color at a certain position indicates the ibd probability that the corresponding founder allele is present . pedimap is being used in several projects in close relation with flexqtl , software for qtl analysis and ibd calculations in multiple pedigreed populations ( bink et al . 2008 ) . in order to allow for easy exchange of data , both pedimap and flexqtl export data in the format required for the other program . in the case of pedimap , this involves the export of data from the complete pedigree or from selected subpopulations , and the filling - in of missing parents of  semi - founders  : individuals of which only 1 parent is known , which are accepted by pedimap but not by flexqtl . in order to import large amounts of snp data generated by illumina s genotyping platforms , a conversion script is available from the pedimap website that builds a data file in pedimap format from a text file exported by the genomestudio software ( http://www.illumina.com/software/ genomestudio_software.ilmn ) . pedimap is available at no cost for the windows platform ( all 32- or 64-bit versions ) . it does not do any calculations such as inbreeding coefficients or ibd probabilities , and it does not offer database capabilities ; it only visualizes the data imported from an input file . however , it does so in a very flexible way and it is unique in its ability to handle a combination of items including selfing , hermaphroditism , backcrossing , polyploidy , and others that are especially important in plant pedigrees . as such it is uniquely suited for use in a plant ( breeding ) context , whereas it can also be applied to other organisms . european projects hidras ( qlk5-ct-2002 - 01492 ; http://www.hidras.unimi.it ) and fruitbreedomics ( 265582-ec - ga ; http://fruitbreedomics.com/ ) ; usda - nifa - scri project rosbreed : enabling marker - assisted breeding in rosaceae ( 2009 - 51181 - 05808 ; http://www.rosbreed.org ) ; wageningen ur department of plant breeding .
pedimap is a user - friendly software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees . 
 genetic data can include marker scores , identity - by - descent probabilities , and marker linkage map positions , allowing the visualization of haplotypes through lineages . 
 the pedigrees can accommodate all types of inheritance , including selfing , cloning , and repeated backcrossing , and all ploidy levels are supported . 
 visual association of the genetic data with phenotypic data simplifies the exploration of large data sets , thereby improving breeding decision making . 
 data are imported from text files ; in addition data exchange with other software packages ( flexqtltm and genomestudiotm ) is possible . 
 instructions for use and an executable version compatible with the windows platform are available for free from http://www.plantbreeding.wur.nl/uk/software_pedimap.html .