+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 displays the alignments in a text format, for
+ example:</p>
+ <p>
+ <pre>
+ FER1_SPIOL/5-13 TTMMGMAT<br />
+ |. .. ||<br />
+ FER1_MESCR/5-15 TAALSGAT
+ </pre>
+ shows the aligned sequences, where '|' links identical residues, and
+ (for peptide) '.' links residues that have a positive PAM250 score.
+ <p>The window also shows information about the alignment such as
+ alignment score, length and percentage identity between the
+ sequences.</p>
+ <p>A button is also provided to allow you to view the sequences as
+ an alignment.</p>
+</body>
+</html>