Figure 1.

Cartoon of the MergeAlign algorithm. In this example, MergeAlign generates a consensus alignment of two sequences A and B, based on five independent MSAs. (A) An example of one of the five constituent MSAs. (B) The numerical representation of the MSA in (A). (C) A graph of the alignment in (A), using the columns of (B) to identify nodes. All edge weights are equal to 1 because only one alignment has been considered. (D) The graph after 4 more MSAs have been added. (E) Each node is given two values: path score/path length. Both are set to 0 for the sink nodes and other nodes are scored recursively. (F) By following the traceback path, the optimum consensus alignment is reconstructed. Each column of the MSA is given a score equal to the weight of the corresponding edge. A full description of the algorithm is given in the methods.