The Alignment Calculations Dialog

The Calculations Dialog (shown above) is opened via the Calculations→Calculate Tree, PCA or PaSiMap... menu entry.

It allows you to select the type of analysis (PCA, Tree, PaSiMap or Pairwise Alignment), and below, the sequence similarity score model that will be used to perform the analysis.

Adding additional score models
Jalview can import substitution matrices in both AAindex and NCBI format (see e.g. ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/). In Jalview 2.10.2, the easiest way to import new models is to drag the score model file onto any alignment window. See the Substitution Matrices Documentation for more information.