Pseudochromosome 1 of
genome, reconstructed from three input maps - optical map with weight of 3, genetic map with weight of 2 and chickpea synteny with weight of 1, to show the capability of ALLMAPS to integrate heterogeneous map types using arbitrary weights. (A) CMAP-style presentation with connecting lines as matching markers. (B) Set of three scatter plots, with each dot representing the physical position on chromosome (x-axis) versus the map location (y-axis). The cM distance along optical map and chickpea comparative map are scaled by 1 cM = 100,000 bp for illustration purposes. This linear transformation does not affect the computation of scaffold configuration. Note that the map based on synteny to chickpea, a divergent species from Medicago, shows the highest level of discordance.