X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=5ae111e9820e8133ee90b7501299b2dda5e830f5;hb=dbd9a22891bded630623f94d78eee8a39f387051;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
+ Pairwise alignment (Proteins only) +
+
+ 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.
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 :
+
+ Gap open : 12
Gap extend : 2
+
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.
++ +