How to understand the color scheme in a sequence alignment?

[Andrew Orry]

Q. How to understand the color scheme in a sequence alignment.

A. 

There are a selection of different alignment coloring schemes you can choose e.g. consensus strength, conservation etc.... Open the Alignment Tools panel  and look for the Color drop down button. Next to this section is a button (see arrow in image below) that will open a table called CONSENSUSCOLOR where you will find the symbols and colors used in the alignment defined.

[Ruben]

If you want to know where does the Color-by menu in the alignment comes from, check the 

CONSENSUSCOLOR.tab table in $ICMHOME

  It contains four columns, and is divided into row sections. 

Columns: AminoAcids,  Color, ConsensusSymbols, ..

For each amino acid, say 'E' you can find two colors depending on the Consensus symbol context in the alignment (3rd column).

For example 'E' in a random position will be color "#ffdddd" , but if the consensus symbol is '-' of 'D' or 'E' or 'q' or 'Q' it will be more bright.

For example the icm-combo color panel is given by:

icm-combo * "" ""
ED "#ffdddd" "" ""
KR "#ddddff" "" ""
WYF "#ffddff" "" ""
WYF "#ff66ff" WYF ""
LVIMA "#eeffee" "" ""
L "#66cd00" L ""
V "#00cd66" V ""
I "#00cd00" I ""
M "#adff2f" M ""
A "#33e500" A ""
G "#99FFFF" G ""
P "#FF9900" P ""
T "#99ffff" "tSTnN#" ""
S "#99ffdd" "tSTnN#aA" ""
N "#99ffee" tnND-gG ""
Q "#99ffee" qQE+- ""
LVIMA "#bbffbb" "#WFY" ""
C "#ffffbb" "" ""
C "#ffff00" C ""
HY "#ffaaff" "#ACFHILMVWYPp" ""
E "#ff3366" -DEqQ ""
D "#ff6699" -DEnNt ""
KR "#33aaff" +KR ""

You may modify, or create your own section. The rules for the consensus derivation are described elsewhere/

Ruben