X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FcolourSchemes%2Fclustal.html;h=0c39a15ba045ccba34e03db9fa646fad4fe95528;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=c15eda45e51e9fb031a92bda09d075f3ba22cd67;hpb=3396e9f33cf3a16a7f38f5163cd057df4b859e7e;p=jalview.git diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html index c15eda4..0c39a15 100755 --- a/help/html/colourSchemes/clustal.html +++ b/help/html/colourSchemes/clustal.html @@ -1,24 +1,125 @@ - -
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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