X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=bb80b84f6dd02ab73498ecb5ee6f5b2d0184e465;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=4ad69ca6f9930823a1e77d9798e8e6cfc90a7937;hpb=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index 4ad69ca..bb80b84 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -1,5 +1,48 @@ - - -Tree - - + + + +Pairwise Alignment + + +

+ 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.

+

 

+ +