X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=fa34db4efdfa8f9b7ca65db6ddd4c847d55abdd4;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=35313306066198e1b210203d97f53e6a9c6d7da6;hpb=3ec000e099e35b359996b824aabeaee632628deb;p=jalview.git diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index 3531330..fa34db4 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -1,21 +1,63 @@ - -
Clustal X
-Clustal X is a graphical interface for the ClustalW multiple sequence alignment - program. Sequences can be coloured either by assigning a colour to specific - residues, or on the basis of an alignment consensus. The residues in each - column are coloured according to the consensus character assigned to that column. - In this way, you can choose to highlight, for example, conserved hydrophilic - or hydrophobic positions in the alignment.
- - + + +Clustal X Colour Scheme
+This is an emulation of the default colourscheme used for alignments in + Clustal X, a graphical interface for the ClustalW multiple sequence alignment + program. Each residue in the alignment is assigned a colour if the + amino acid profile of the alignment at that position + meets some minimum criteria specific for the residue type.
+The table below gives these criteria as clauses: {+X%,xx,y}, + where X is the minimum percentage presence for any of the xx (or y) residue types.
+
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