The "Edit guide tree file" panel. The guide tree file used by iSGv2.1 contains the partition-specific parameters. Using the "Edit guide tree file" panel users can set all necessary parameters including the guide tree. In this example, the MSA-root file for the lipocalin superfamily contains the alignment obtained from Sánchez et al. . Indel options are also set as shown. The guide tree can be edited either by editing the tree in Newick format or by using an interactive graphical display (see Figure 6).
Anderson et al. BMC Bioinformatics 2011 12:184 doi:10.1186/1471-2105-12-184