#Palette:

#color                     : #RGB
color black                : #000000
color white                : #ffffff
color red                  : #ff0000
color green                : #00ff00
color blue                 : #0000ff
color cyan                 : #00ffff
color magenta              : #ff00ff
color yellow               : #ffff00
color purple               : #6600cc
color dull-blue            : #0099ff
color dark-green-blue      : #33cccc
color medium-green-blue    : #00ffcc
color bright-blue          : #0033ff
color dark-green           : #009900
color bright-green         : #33cc00
color orange               : #ff3333
color orange-brown         : #cc6600
color bright-red           : #cc0000
color light-gray           : #999999
color dark-gray            : #666666
color gray0                : #ffffff
color gray1                : #eeeeee
color gray2                : #dddddd
color gray3                : #cccccc
color gray4                : #bbbbbb
color gray5                : #aaaaaa
color gray6                : #999999
color gray7                : #888888
color gray8                : #777777
color gray9                : #666666
color gray10               : #555555
color gray11               : #444444
color gray12               : #333333
color gray13               : #222222
color gray14               : #111111
color gray15               : #000000
color clustal-red          : #e53319
color clustal-blue         : #197fe5
color clustal-green        : #19cc19
color clustal-cyan         : #19b2b2
color clustal-pink         : #e57f7f
color clustal-magenta      : #cc4ccc
color clustal-yellow       : #cccc00
color clustal-orange       : #e5994c
color clustal-white        : #ffffff
color clustal-light-gray   : #999999
color clustal-dark-gray    : #666666
color clustal-black        : #000000
color clustal-white-print  : #ffffff
color clustal-yellow-print : #ffff00
color clustal-violet-print : #6619e5
color clustal-red-print    : #e57f66
color clustal-blue-print   : #66e5e5
color clustal-purple-print : #b299e5
color clustal-black-print  : #000000
color clustal-pink-print   : #e57f7f
color clustal-cyan-print   : #19b2b2
color clustal-magenta-print : #cc4ccc
color clustal-orange-print : #e5994c
color clustal-green-print  : #19cc19
color clustal-light-gray-print : #999999
color clustal-dark-gray-print : #99b2b2
color nardi-red            : #ff1111
color nardi-blue           : #1155ff
color nardi-green          : #11dd11
color nardi-cyan           : #11ffff
color nardi-yellow         : #ffff11
color nardi-orange         : #ff7f11
color nardi-pink           : #ff11ff
color nardi-purple         : #6611cc
color nardi-dull-blue      : #197fe5
color nardi-dark-gray      : #666666
color nardi-light-gray     : #999999
color lin-A                : #90fe23
color lin-R                : #fe5e2d
color lin-N                : #2e3d2d
color lin-D                : #00903b
color lin-C                : #004baa
color lin-Q                : #864b00
color lin-E                : #3fa201
color lin-G                : #10fe68
color lin-H                : #b2063b
color lin-I                : #04ced9
color lin-L                : #4972fe
color lin-K                : #c4a100
color lin-M                : #2a84dd
color lin-F                : #a60ade
color lin-P                : #fe61fe
color lin-S                : #f7e847
color lin-T                : #fefeb3
color lin-W                : #4a007f
color lin-Y                : #e903a8
color lin-V                : #5bfdfd


#Colormap listing - suitable for reloading.
#Character matching is case-sensitive.

[CCLUSTAL]
#Protein consensus: highlight equivalence class
#symbols =>  color                #comment
*        ->  nardi-dark-gray      #mismatch
+        ->  nardi-red            #positive charge
-        ->  nardi-pink           #negative charge
a        ->  nardi-dull-blue      #aromatic
c        ->  nardi-purple         #charged
h        ->  nardi-dull-blue      #hydrophobic
l        ->  nardi-dull-blue      #aliphatic
o        ->  nardi-green          #alcohol
p        ->  nardi-green          #polar
s        ->  nardi-blue           #small
t        ->  nardi-blue           #turnlike
u        ->  nardi-blue           #tiny

[CHARGE]
#Protein: highlight charged amino acids
#symbols =>  color                #comment
*        =>  black                #mismatch
?        =>  light-gray           #unknown
Bb       =>  dark-gray            #D or N
Dd       =>  bright-blue          #negative charge
Ee       =>  bright-blue          #negative charge
Kk       =>  bright-red           #positive charge
Rr       =>  bright-red           #positive charge
Xx       =>  dark-gray            #any
Zz       =>  dark-gray            #E or Q

[CLUSTAL]
#Protein: highlight amino acid physicochemical properties
#symbols =>  color                #comment
*        =>  clustal-dark-gray    #mismatch
?        =>  clustal-light-gray   #unknown
Aa       =>  clustal-blue         #hydrophobic
Bb       =>  clustal-white        #D or N
Cc       =>  clustal-pink         #hydrophobic
Dd       =>  clustal-magenta      #negative charge
Ee       =>  clustal-magenta      #negative charge
Ff       =>  clustal-blue         #large hydrophobic
Gg       =>  clustal-orange       #glycine
Hh       =>  clustal-cyan         #large hydrophobic
Ii       =>  clustal-blue         #hydrophobic
Kk       =>  clustal-red          #positive charge
Ll       =>  clustal-blue         #hydrophobic
Mm       =>  clustal-blue         #hydrophobic
Nn       =>  clustal-green        #polar
Pp       =>  clustal-yellow       #proline
Qq       =>  clustal-green        #polar
Rr       =>  clustal-red          #positive charge
Ss       =>  clustal-green        #small alcohol
Tt       =>  clustal-green        #small alcohol
Vv       =>  clustal-blue         #hydrophobic
Ww       =>  clustal-blue         #large hydrophobic
Xx       =>  clustal-dark-gray    #any
Yy       =>  clustal-cyan         #large hydrophobic
Zz       =>  clustal-white        #E or Q

[CLUSTAL_NUC]
#CLUSTAL-derived colours for nucleotides
#symbols =>  color                #comment
*        =>  clustal-dark-gray    #mismatch
?        ->  clustal-light-gray   #unknown
Aa       =>  clustal-red          #match
Bb       =>  clustal-dark-gray    #match
Cc       =>  clustal-blue         #match
Dd       =>  clustal-dark-gray    #match
Gg       =>  clustal-orange       #match
Hh       =>  clustal-dark-gray    #match
Kk       =>  clustal-dark-gray    #match
Mm       =>  clustal-dark-gray    #match
Nn       =>  clustal-dark-gray    #match
Rr       =>  clustal-dark-gray    #match
Ss       =>  clustal-dark-gray    #match
Tt       =>  clustal-green        #match
Uu       =>  clustal-green        #match
Vv       =>  clustal-dark-gray    #match
Ww       =>  clustal-dark-gray    #match
Xx       =>  clustal-dark-gray    #match
Yy       =>  clustal-dark-gray    #match

[CYS]
#Protein: highlight cysteines
#symbols =>  color                #comment
*        ->  dark-gray            #mismatch
?        ->  light-gray           #unknown
Cc       =>  yellow               #cysteine
Xx       ->  dark-gray            #any

[D1]
#DNA: highlight nucleotide types
#symbols =>  color                #comment
*        ->  dark-gray            #mismatch
?        ->  light-gray           #unknown
Aa       =>  bright-blue          #purine
Bb       =>  dark-gray            #C or G or T; not A
Cc       =>  dull-blue            #pyrimidine
Dd       =>  dark-gray            #A or G or T; not C
Gg       =>  bright-blue          #purine
Hh       =>  dark-gray            #A or C or T; not G
Kk       =>  dark-gray            #G or T
Mm       =>  dark-gray            #A or C
Nn       =>  dark-gray            #A or C or G or T
Rr       =>  dark-gray            #A or G
Ss       =>  dark-gray            #C or G
Tt       =>  dull-blue            #pyrimidine
Uu       =>  dull-blue            #pyrimidine
Vv       =>  dark-gray            #A or C or G; not T
Ww       =>  dark-gray            #A or T
Xx       ->  dark-gray            #any
Yy       =>  dark-gray            #C or T

[D2]
#DNA: highlight match versus mismatch under consensus coloring schemes
#symbols =>  color                #comment
*        =>  bright-red           #mismatch
?        ->  light-gray           #unknown
Aa       =>  bright-blue          #match
Bb       =>  bright-blue          #match
Cc       =>  bright-blue          #match
Dd       =>  bright-blue          #match
Gg       =>  bright-blue          #match
Hh       =>  bright-blue          #match
Kk       =>  bright-blue          #match
Mm       =>  bright-blue          #match
Nn       =>  bright-blue          #match
Rr       =>  bright-blue          #match
Ss       =>  bright-blue          #match
Tt       =>  bright-blue          #match
Uu       =>  bright-blue          #match
Vv       =>  bright-blue          #match
Ww       =>  bright-blue          #match
Xx       =>  bright-blue          #match
Yy       =>  bright-blue          #match

[DC1]
#DNA consensus: highlight ring type
#symbols =>  color                #comment
*        ->  dark-gray            #mismatch
r        ->  purple               #purine
y        ->  orange               #pyrimidine

[GPCR]
#Protein: GPCRdb color scheme for Gert Vriend
#symbols =>  color                #comment
*        ->  dark-gray            #mismatch
?        ->  light-gray           #unknown
Aa       =>  bright-green         #hydrophobic
Bb       =>  bright-red           #D or N
Cc       =>  yellow               #cysteine
Dd       =>  bright-red           #positive charge
Ee       =>  bright-red           #positive charge
Ff       =>  cyan                 #large hydrophobic
Gg       =>  orange-brown         #backbone change
Hh       =>  bright-blue          #negative charge
Ii       =>  bright-green         #hydrophobic
Kk       =>  bright-blue          #negative charge
Ll       =>  bright-green         #hydrophobic
Mm       =>  bright-green         #hydrophobic
Nn       =>  bright-red           #positive charge
Pp       =>  orange-brown         #backbone change
Qq       =>  bright-red           #positive charge
Rr       =>  bright-blue          #negative charge
Ss       =>  dark-green-blue      #small alcohol
Tt       =>  dark-green-blue      #small alcohol
Vv       =>  bright-green         #hydrophobic
Ww       =>  cyan                 #large hydrophobic
Xx       ->  dark-gray            #any
Yy       =>  medium-green-blue    #large hydrophobic
Zz       =>  bright-red           #E or Q

[KXLIN]
#Kuang Lin's colour neural net derived scheme
#symbols =>  color                #comment
*        ->  dark-gray            #mismatch
?        ->  light-gray           #unknown
Aa       =>  lin-A                
Bb       =>  dark-gray            #D or N
Cc       =>  lin-C                
Dd       =>  lin-D                
Ee       =>  lin-E                
Ff       =>  lin-F                
Gg       =>  lin-G                
Hh       =>  lin-H                
Ii       =>  lin-I                
Kk       =>  lin-K                
Ll       =>  lin-L                
Mm       =>  lin-M                
Nn       =>  lin-N                
Pp       =>  lin-P                
Qq       =>  lin-Q                
Rr       =>  lin-R                
Ss       =>  lin-S                
Tt       =>  lin-T                
Vv       =>  lin-V                
Ww       =>  lin-W                
Xx       ->  dark-gray            #any
Yy       =>  lin-Y                
Zz       =>  dark-gray            #E or Q

[NARDI]
#Protein: highlight amino acid physicochemical properties
#symbols =>  color                #comment
*        =>  nardi-dark-gray      #mismatch
?        =>  nardi-light-gray     #unknown
Aa       =>  nardi-dull-blue      #hydrophobic
Bb       =>  nardi-pink           #D or N
Cc       =>  nardi-yellow         #cysteine
Dd       =>  nardi-pink           #negative charge
Ee       =>  nardi-pink           #negative charge
Ff       =>  nardi-dull-blue      #large hydrophobic
Gg       =>  nardi-orange         #glycine
Hh       =>  nardi-dull-blue      #large hydrophobic
Ii       =>  nardi-dull-blue      #hydrophobic
Kk       =>  nardi-red            #positive charge
Ll       =>  nardi-dull-blue      #hydrophobic
Mm       =>  nardi-dull-blue      #hydrophobic
Nn       =>  nardi-green          #polar
Pp       =>  nardi-yellow         #proline
Qq       =>  nardi-green          #polar
Rr       =>  nardi-red            #positive charge
Ss       =>  nardi-green          #small alcohol
Tt       =>  nardi-green          #small alcohol
Vv       =>  nardi-dull-blue      #hydrophobic
Ww       =>  nardi-dull-blue      #large hydrophobic
Xx       =>  nardi-dark-gray      #any
Yy       =>  nardi-cyan           #large hydrophobic
Zz       =>  nardi-pink           #E or Q

[P1]
#Protein: highlight amino acid physicochemical properties
#symbols =>  color                #comment
*        ->  dark-gray            #mismatch
?        ->  light-gray           #unknown
Aa       =>  bright-green         #hydrophobic
Bb       =>  dark-gray            #D or N
Cc       =>  yellow               #cysteine
Dd       =>  bright-blue          #negative charge
Ee       =>  bright-blue          #negative charge
Ff       =>  dark-green           #large hydrophobic
Gg       =>  bright-green         #hydrophobic
Hh       =>  dark-green           #large hydrophobic
Ii       =>  bright-green         #hydrophobic
Kk       =>  bright-red           #positive charge
Ll       =>  bright-green         #hydrophobic
Mm       =>  bright-green         #hydrophobic
Nn       =>  purple               #polar
Pp       =>  bright-green         #hydrophobic
Qq       =>  purple               #polar
Rr       =>  bright-red           #positive charge
Ss       =>  dull-blue            #small alcohol
Tt       =>  dull-blue            #small alcohol
Vv       =>  bright-green         #hydrophobic
Ww       =>  dark-green           #large hydrophobic
Xx       ->  dark-gray            #any
Yy       =>  dark-green           #large hydrophobic
Zz       =>  dark-gray            #E or Q

[PC1]
#Protein consensus: highlight equivalence class
#symbols =>  color                #comment
*        ->  dark-gray            #mismatch
+        ->  bright-red           #positive charge
-        ->  bright-blue          #negative charge
a        ->  dark-green           #aromatic
c        ->  purple               #charged
h        ->  bright-green         #hydrophobic
l        ->  bright-green         #aliphatic
o        ->  dull-blue            #alcohol
p        ->  dull-blue            #polar
s        ->  bright-green         #small
t        ->  bright-green         #turnlike
u        ->  bright-green         #tiny

[POLAR1]
#Protein: highlight charged and polar amino acids
#symbols =>  color                #comment
*        ->  dark-gray            #mismatch
?        ->  light-gray           #unknown
Bb       =>  purple               #D or N
Dd       =>  bright-blue          #negative charge
Ee       =>  bright-blue          #negative charge
Hh       =>  purple               #charged/polar
Kk       =>  bright-red           #positive charge
Nn       =>  purple               #charged/polar
Qq       =>  purple               #charged/polar
Rr       =>  bright-red           #positive charge
Ss       =>  purple               #charged/polar
Tt       =>  purple               #charged/polar
Xx       ->  dark-gray            #any
Zz       =>  purple               #E or Q

# MView 1.55, Copyright (C) 1997-2013 Nigel P. Brown
