Figure 4

Setting simulation parameters. Parameters for the iSGv2.1 simulation are set in the "Basic parameters" panel (A) and in the "Advanced parameters" panel (B). In the "Basic parameters" panel, the guide tree file is set to "lipocalinSuperFamily.tree". The file format, output file name prefix, output files, as well as the sequence type and substitution model are set in this page. In the "Advanced parameters" page, the lineage specification file, which contains the motifs to be applied to the simulation, is selected. The alpha constant for the Gamma distribution is set to 3.88 and the amino acid frequencies are set as shown in this example.