X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=edd0ae4e71696fd72cc5c80b0f061807adc76159;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=4ad69ca6f9930823a1e77d9798e8e6cfc90a7937;hpb=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index 4ad69ca..edd0ae4 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -1,5 +1,38 @@ - - -Tree - - + + +Pairwise Alignment + +

Pairwise alignment (Proteins only)

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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.

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