<html>\r
+<head><title>Pairwise Alignment</title></head>\r
<body>\r
-Tree \r
+<p><strong>Pairwise alignment (Proteins only)</strong></p>\r
+<p>This calculation is performed on the selected sequences only. Java is not the\r
+ fastest language in the world and aligning more than a handful of sequences\r
+ will take a fair amount of time. <br>\r
+ For each pair of sequences the best global alignment is found using BLOSUM62\r
+ as the scoring matrix. The scores reported are the raw scores. The sequences\r
+ are aligned using a dynamic programming technique and using the following gap\r
+ penalties : </p>\r
+<p>Gap open : 12 <br>\r
+ Gap extend : 2 </p>\r
+<p>When you select the pairwise alignment option a new window will come up which\r
+ will display the alignments in a text format as they are calculated. Also displayed\r
+ is information about the alignment such as alignment score, length and percentage\r
+ identity between the sequences.</p>\r
+<p> </p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff