X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2FwebServices%2Fclustalw.html;h=cbfc115de506de860804e2eeac489c48132b8ff4;hb=c53aeee9a688f68d64106a968876e542f701fbc6;hp=325849414c536606491990cbc53978a601b5bfc6;hpb=c30bcb5bc195374ef89916a1c39e4812fa93bf4c;p=jalview.git
diff --git a/help/html/webServices/clustalw.html b/help/html/webServices/clustalw.html
index 3258494..cbfc115 100755
--- a/help/html/webServices/clustalw.html
+++ b/help/html/webServices/clustalw.html
@@ -1,31 +1,45 @@
-
-ClustalW Alignment
-
-ClustalW Alignments
-ClustalW is a program for multiple sequence alignment. It works
-with both DNA and protein sequences, and can also perform profile
-profile alignments to align two or more multiple sequence
-alignments.
-
-Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994)
-CLUSTAL W: improving the sensitivity of progressive multiple
-sequence alignment through sequence weighting, position specific gap
-penalties and weight matrix choice.
-Nucleic Acids Research 22 4673-4680
-
-There are two versions of this alignment function, which will operate
-on the selected region, if any, or the whole sequence set:
-
-- Calculations→Web Service→Clustal
-Alignment..
-Aligns using the clustalW program, ignoring any gaps in the submitted
-sequence set.
-
-- Calculations→Web Service→Clustal
-Realign..
-Submits the sequences with existing gaps to clustalW, which will
-preserve existing gaps and re-align those regions which are not optimal.
-
-
-
-
+
+
+ClustalW Alignment
+
+ClustalW Alignments
+ClustalW is a program for multiple sequence alignment. It works
+with both DNA and protein sequences, and can also perform profile
+profile alignments to align two or more multiple sequence
+alignments.
+
+Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994)
+CLUSTAL W: improving the sensitivity of progressive multiple
+sequence alignment through sequence weighting, position specific gap
+penalties and weight matrix choice.
+Nucleic Acids Research 22 4673-4680
+
+There are two versions of this alignment function, which will operate
+on the selected region, if any, or the whole sequence set:
+
+ - Web Service→Alignment→ClustalW Multiple Sequence Alignment
+ Aligns using the clustalW program, ignoring any gaps in the submitted sequence
+ set.
+ - Web Service→Alignment→ClustalW Mulitple Sequence Alignment
+ Realign
+ Submits the sequences with existing gaps to clustalW, which will preserve
+ existing gaps and re-align those regions which are not optimal.
+
+
+