The Topology Structure tabbed pane allows you to define a prediction about the topology structure of the alignment before the analysis actually runs.
By default, the table will already contain TOPALi's estimated structure for the alignment. This can be overwritten by selecting the Edit the topology structure checkbox
Adding new structure partitions
To add a new structure partition, first click the Add Breakpoint button. This will add a new record to the table that must be further edited to complete the definition.
The Breakpoint field defines where the nucleotide position where the new partition will end. Partitions are assumed to start either from the beginning of the alignment, or from the end of the preceding partition if a partition already exists whose endpoint value is lower than the new partition's.
The Topology field defines what the topology for the new partition will be. As there are only 4 sequences, the maximum of tree topologies is 3, and one of these 3 must be chosen. The topologies are listed as 1, 2, and 3, along with the names of the sequences that form them.
Once a new partition has been added, the graphical display of the alignment's topology structure will update to reflect the changes you have made. This display provides a simple way of visualizing the data entered into the table, with each of the three possible topologies colour-coded to its own unique colour.
Removing existing structure partitions
To remove an existing structure partition, first select it within the table, then click the Remove Breakpoint button.
Resetting the structure
If you want to reset the topology structure to its original TOPALi-defined state, or if the structure displayed is no longer valid (perhaps because difference sequences have selected since the last HMM run), then click the Regenerate button to achieve this.