From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 3 Aug 2017 13:05:14 +0000 (+0100)
Subject: JAL-2418 what’s new - faster PCA, calculations UI and score model framework
X-Git-Tag: Release_2_10_2~3^2~15^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ce6edf5c9421ce38f625886885ed2cd8f506f08d;p=jalview.git

JAL-2418 what’s new - faster PCA, calculations UI and score model framework
---

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 4b82179..8a0436d 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -32,6 +32,15 @@
     highlights are below.
   </p>
   <ul>
+    <li><strong>New UI, and faster and more configurable implementation for PCA, Neighbour-Joining and UPGMA Trees</strong><br>
+      Menu entries for calculating PCA and different types of tree have
+      been replaced by a single <em>Calculations</em> dialog box. The
+      underlying implementation for the PCA and tree calculations have been
+      made faster and more memory efficient. A new framework has also been
+      created for the score models used to calculate distances between
+      sequences. This framework allows import of substitution matrices in
+      NCBI and AAIndex format, and custom score models to be created via a
+      groovy script.</li>
     <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
       alignment, protein conservation analysis, and protein disorder and
       RNA secondary structure prediction services are now provided by <a