Figure 2

WAMI main web-interface. The upper sections include input of maps and cost file as well as some examples. A description of the example of the President Jefferson's dataset is shown. The lower section sets the option for building a phylogenetic tree over the input map. Note that there are other related tabbed pages, including introduction, web-service, download, and help/Blog pages. Right: The result page of WAMI. The output is organized into three categories: Alignment, phylogeny, and batch retrieval. In the alignment category, all pairwise alignments can be displayed. Here, an alignment between maps one and two (given in the left screen shot) is visualized. The replaced (match/mismatch) units are put above each other. An arc connecting two identical units corresponds to a duplication event, and an arc connecting two different units corresponds to a duplication followed by a mutation events. The sub-map composed of the units " bcaccbb" of the lower sequence emerged from the leftmost unit b of this sub-map. The duplication history was the one explained in the subsection about duplication history and alignment model. The category showing the phylogenetic tree appears only if this option was set. We provide the tree in text, JPEG (shown image), and PDF format. Finally, we provide a link to a compressed file containing all the input/output files of a WAMI run.