X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=0e57626435815ca62d1fb5463243f57935a2330b;hb=0696cffbccbb537be78d9fc2410589adbcd7be35;hp=655464356e2b8caa018ae3445aa71b057522e812;hpb=1693646e78fb0dddebcd94f8bef7e2acd3bdaae0;p=jalview.git diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index 6554643..0e57626 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -1,24 +1,62 @@ - -
- - - - -Clustal X
-Clustal X is a graphical interface for the ClustalW multiple sequence alignment - program. Sequences can be colored either by assigning a color to specific - residues, or on the basis of an alignment consensus. The residues in each - column are colored 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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