X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fconservation.html;h=37804bcc1e7430b49508fdec3c28cdc3d3600e6b;hb=6fbc6ebb2f261d9071e40fcf51b02584a2119aa2;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
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*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see
Colouring by Conservation
+This is an approach to alignment colouring which highlights + regions of an alignment where physicochemical properties are + conserved. It is based on the one used in + the AMAS method of multiple sequence alignment analysis (Livingstone + C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy + for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 + No. 6 (745-756)). See the conservation calculation help page for + a more thorough explanation of the calculation. +
+For an already coloured alignment, the conservation index at each + alignment position is used to modify the shading intensity of the + colour at that position. This means that the most conserved columns + in each group have the most intense colours, and the least conserved + are the palest. The slider controls the contrast between these + extremes.
+Conservation can be calculated over all sequences in an alignment, or just + within specific groups (such as those defined by + phylogenetic tree partitioning). + The option 'apply to all groups' controls whether the contrast + slider value will be applied to the indices for the currently + selected group, or all groups defined over the alignment.
+ +