X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fclustalw.html;h=81ccc4e28ddf4415ed8a7f4d99f7a8ebe3ceaaf4;hb=0696cffbccbb537be78d9fc2410589adbcd7be35;hp=96b45b77cd78285398b26371d201bf8a96cb087e;hpb=ac5cc638b08386985f91503c81b27263230046e3;p=jalview.git
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@@ -1,28 +1,46 @@
-
-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.
-
-
-
+
+
+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.
+
+As of Jalview 2.6, alignment services accessed via the 'Alignment' submenu should be considered legacy Jalview SOAP services.
+
+