Endelman BMC Genomics 2011, 12:407 http://www.biomedcentral.com/1471-2164/12/407 Page 6 of 9 Figure 2 Simplified consensus graphs of the barley 5HS telomere. Marker labels are shown within each vertex, and markers for genes at the hardness locus are indicated (hinb/hina/gsp). On the left side of the figure is the ordinal consensus graph produced by DAGGER, in which there is a path from vertex v to vertex w if and only if v mapped before w in one of the linkage maps. On the right side is the simplified consensus graph produced by MergeMap. Comparison with Table 2, which contains the linkage maps for the 5HS telomere, confirms that the output from DAGGER is ordinally equivalent to the linkage maps, while the output from MergeMap is not. In particular, the simplified graph from MergeMap contains several unphysical relationships for the hardness locus markers. average correlation coefficient between the two maps was 0.95 on a scale of 10 cM, indicating a high degree of similarity. Nonetheless, there were several indications of improved fine structure with DAGGER. Figure 3 com- pares the two (rescaled) consensus maps at the 5HS tel- omere. On the physical map the hardness locus (hinb to gsp) is 110 kb, within which there was only 1 recombi- nant out of the 278 total individuals in the SM, OWB, and MB populations [11]. This is reflected in the linkage maps in Table 2, where all the hardness locus markers appear in one bin in both the SM and MB linkage maps and in two bins separated by 1.1 cM in the OWB linkage map. From these data the hardness locus should occupy less than 1 cM in the consensus map, which was true with DAGGER (0.8 cM interval) but not with Mer- geMap (4.2 cM interval). Figure 4 shows the RMS error between the consensus map and the linkage maps for each of the seven barley chromosomes. The DAGGER map had consistently less error, with an average of 0.82 cM per marker interval compared to 2.28 cM with MergeMap. Conclusions New algorithms for the simplification and linearization of consensus graphs have been implemented as a