**The Alignment Calculations Dialog**

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

It allows you to select the type of alignment analysis calculation (PCA or Tree), and 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.