X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fconservation.html;h=88ef6ba4cc7d6d66ab10dc2dc4e03adf31a233cc;hb=2b5b5218e86b959ea593fd656c4f87d75c49911f;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/colourSchemes/conservation.html b/help/html/colourSchemes/conservation.html index e18e273..88ef6ba 100755 --- a/help/html/colourSchemes/conservation.html +++ b/help/html/colourSchemes/conservation.html @@ -1,18 +1,55 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> + +Colouring by Conservation + + +

+ 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. +

+ +