Summary information

Summary information for an alignment file can be displayed by selecting Alignment | Display Summary Info from the menu bar. This brings up the Summary Information dialog.

Note that certain parameters must be estimated by TOPALi the first time they are accessed. This may happen after requesting the Summary Information dialog, in which case a short delay may be evident before the dialog appears.

The dialog displays the following information:

• Original name of the alignment
• Alignment length
• Number of sequences
• Alignment data type (for example nucleotide or protein)
• Whether any sequences are identical (and their names if they are)
• Nucleotide frequencies
• Average pairwise distance
• Transition/transversion ratio (based on F84+Gamma)
• Alpha shape parameter (based on F84+Gamma)