<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * 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/>.
+ * 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>
+ -->
+<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>
+ <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