- <!-- JAL-789,JAL-4257 --> allow adjustment of gap opening, extension, and score model for built in pairwise alignment
- <!-- JAL-4447 --> Pairwise alignment can be performed with different substitution matrices
- <!-- JAL-4447 --> PCA, Pairwise alignment, trees and PaSiMap window titles include the matrix and additional parameters used
+- <!-- JAL-4461 --> "Select format by extension" option in Jalview's "Save As" dialog's file type dropdown menu
### Experimental Features (enable via Desktop's tools menu)