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