* 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 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>