X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Fconservation.html;h=ccd361503001d0762f83ba134938de3abda2810b;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=cad40a7943ea778d5c256d2a2d9e13434aafd970;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git diff --git a/help/html/colourSchemes/conservation.html b/help/html/colourSchemes/conservation.html index cad40a7..ccd3615 100755 --- a/help/html/colourSchemes/conservation.html +++ b/help/html/colourSchemes/conservation.html @@ -1,44 +1,56 @@ -Colouring by Conservation + * 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.

+

+ 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. +