X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=2900fa4180ddacac7651fa0be84fc27e55b2ab2f;hb=07e6452f0883636e9439327ac8fece19b0461537;hp=7c5f7a8852b9d15eb9270872d80a72a1120ca847;hpb=8e55529daa9d811b947a0847969ba171fc26b690;p=jalview.git diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index 7c5f7a8..2900fa4 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -1,21 +1,62 @@ - -
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 hydrophylic - 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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