-<html>\r
-<body>\r
-Tree \r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<head><title>Pairwise Alignment</title></head>
+<body>
+<p><strong>Pairwise alignment (Proteins only)</strong></p>
+<p>This calculation is performed on the selected sequences only. Java is not the
+ fastest language in the world and aligning more than a handful of sequences
+ will take a fair amount of time. <br>
+ For each pair of sequences the best global alignment is found using BLOSUM62
+ as the scoring matrix. The scores reported are the raw scores. The sequences
+ are aligned using a dynamic programming technique and using the following gap
+ penalties : </p>
+<p>Gap open : 12 <br>
+ Gap extend : 2 </p>
+<p>When you select the pairwise alignment option a new window will come up which
+ will display the alignments in a text format as they are calculated. Also displayed
+ is information about the alignment such as alignment score, length and percentage
+ identity between the sequences.</p>
+<p> </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff