Figure 6.

Screenshot of analysis options on SynMap. The whole synteny pipeline contains a few components, streamlined by QUOTA-ALIGN: 1) chaining anchors; 2) 2D overlapping block merging; 3) screening of synteny blocks. In the example shown, we are only interested in orthologous blocks between A. thaliana and A. lyrata, therefore a quota of 1:1 is used here. "Overlap distance parameter" is also known as Nm in the Methods; 4) encoding of the order for the screened blocks is automatically sent to the GRIMM server [27] for rearrangement analysis.