Generating reports

TOPALi contains the ability to automatically generate HTML-formatted reports based on the results obtained from running PDM, HMM, or DSS analysis methods on an alignment.

Note that reports can only be generated on result sets that contain threshold levels (hence multiple run DSS results cannot be used to generate a report).

Selecting the result set

To generate a report, you must first select the results to use. This is done via the Generate Report dialog, accessible by selecting Analysis | Generate Report from the menu bar, clicking the Generate Report toolbar button, or pressing Ctrl-R.

Generate Report

This dialog allows you to specify several settings. Firstly, a location on disk where the report will be stored.

You can then choose whether or not to include mosaic structure predictions.

• Include mosaic structure predictions in this report - if selected, TOPALi will run full mosaic structure prediction calculations during the creation of the report. As these calculations require the user of Fitch/DSS to estimate which sequences are mosaic, this process may take some time.

Finally, the source data (results) that will be used to generate the report.

• Generate from a new PDM analysis run - creates the report by allowing you to run PDM over the alignment, automatically generating the report once the analysis is complete.
• Generate from a new HMM analysis run - creates the report by allowing you to run HMM over the alignment, automatically generating the report once the analysis is complete.
• Generate from a new DSS analysis run - creates the report by allowing you to run DSS over the alignment, automatically generating the report once the analysis is complete.
• Use results from a previous run - creates the report by allowing you to select from an existing set of results.

If the report is to be generated from a new PDM, HMM, or DSS run, then the appropriate dialog for specifying that analysis method's settings will open once the Generate button has been clicked. For further information on these dialogs, see the PDM, HMM, or DSS user manual pages.

Creating the report

As the report is being generated, the Generating Report dialog appears to show you its progress.

Note that the trees created from the partitions that are selected will be created using the tree settings specified in the Analysis Settings dialog (see analysis settings help for further information on this).

Once the report is complete, you will have the final option of automatically populating the Partitions dialog with the partitions that were selected for the report.

The report then appears in the Report pane of the main window, in addition to being saved to disk in the location specified earlier. If you wish to print the report from within TOPALi, see printing for further information.