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When SIMMAP 1.5 reads trees into memory it automatically converts the trees (if rooted) to being unrooted and assigns an arbitrary root position for displaying them in the Tree View window. Often users will want to infer the character changes in a rooted, or polarized, fashion to better understand the direction of character evolution. Trees can be rooted in SIMMAP 1.5 by defining an outgroup. The outgroup can consist of one or more taxa and a number of different options for dealing with the outgroup during mutational mapping can be selected. To root the trees select Trees->Root Trees... and the following window will be displayed.

To select outgroup species (sequences) simply select their names in the Ingroup table and click the Outgroup button. To move them back to the ingroup select the names in the Outgroup table and click the Ingroup button. All trees loaded in memory will be rooted if the outgroup is valid. Otherwise the user will be notified and asked whether the tree should be left unchanged, or the action cancelled.

The following options are available:

1. Include outgroup lineages when simulating character maps: This option uses the character state information in the outgroup species when simulating character maps.
2. Exclude outgroup lineages when simulating character maps: This option does not use the outgroup character state information when simulating character maps, but simply uses the outgroup to establish the root position.

Trees can be derooted to the original configuration found in the input file by selecting Trees->Deroot Trees from the application menu.