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+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%% %%%%%
+%%%%% Default parameter settings for the LaTeX ``TeXshade'' package %%%%%
+%%%%% %%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%% %%%%%
+%%%%% This example file contains all standard settings of the TeXshade %%%%%
+%%%%% package. It can be used as a template for the creation of perso- %%%%%
+%%%%% nal parameter files. All TeXshade user commands are allowed and %%%%%
+%%%%% functional when specified here. %%%%%
+%%%%% %%%%%
+%%%%% To activate these settings for your alignment load this file by %%%%%
+%%%%% naming it as optional parameter at the beginning of the texshade %%%%%
+%%%%% environment, e.g. %%%%%
+%%%%% %%%%%
+%%%%% \begin{texshade}[myparameterfile]{alignmentfile} %%%%%
+%%%%% . %%%%%
+%%%%% . %%%%%
+%%%%% \end{texshade} %%%%%
+%%%%% %%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\shadingmode{identical} % Shade identical residues only
+\shadingcolors{blues} % Select the blue color scheme for shading
+\constoallseqs % Calculate consensus considering all seqs
+\threshold{50} % Consensus threshold percentage is 50
+\residuesperline{999} % As many residues as possible per line
+\numberingwidth{9999} % Assign space for 4 digit numbering
+\charstretch{1.15} % Stretch character width 1.15fold
+\linestretch{1} % Do not stretch lines
+\gapchar{.} % . is printed in sequence gaps
+\gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt
+\gapcolors{Black}{White} % Gap symbols appear `Black on White'
+\numberingcolor{Black} % Numbering color is `Black'
+\shownumbering{left} % Show sequence numbering on the left
+\namescolor{Black} % Names' color is `Black'
+\shownames{right} % Show sequence names on the right
+\consensuscolors{Black}{White} % All consensus symbols/letters
+ {Black}{White} % appear `Black on White'
+ {Black}{White} %
+\showconsensus{bottom} % Show consensus line at bottom with
+\defconsensus{{}}{*}{!} % Blank =no match; * =match; ! =all match
+\rulercolor{Black} % Ruler's color is `Black'
+\hideruler % Do not show the ruler
+\showleadinggaps % Show gap symbols before sequence start
+\rulersteps{10} % Ruler ticks every 10 residues
+\legendcolor{Black} % Legend text color is `Black'
+\hidelegend % Do not show the legend
+\alignment{center} % Center alignment on page
+\medsepline % Medium height if separation line is on
+\medblockskip % Medium skip between sequence blocks
+\flexblockspace % Use optimized space between blocks
+\featurerule{0.5ex} % Set feature rule thickness to 1/5 ex
+\bargraphstretch{1} % Do not stretch bars in feature graphs
+\colorscalestretch{1} % Do not stretch color scales in features
+\backtranstext{horizontal} % Horizontal triplets in feature texts
+\backtranslabel{alternating} % Alternating triplets in feature styles
+\setfamily{residues}{tt} % Use typewriter family for residues
+\setseries{residues}{md} % Use normal series for residues
+\setshape {residues}{up} % Use upright shape for residues
+\setsize {residues}{normalsize} % Use normal size for residues
+\setfamily{numbering}{tt} % Use typewriter family for numbering
+\setseries{numbering}{md} % Use normal series for numbering
+\setshape {numbering}{up} % Use upright shape for numbering
+\setsize {numbering}{normalsize} % Use normal size for numbering
+\setfamily{names}{tt} % Use typewriter family for names
+\setseries{names}{md} % Use normal series for names
+\setshape {names}{up} % Use upright shape for names
+\setsize {names}{normalsize} % Use normal size for names
+\setfamily{features}{rm} % Use roman family for feature texts
+\setseries{features}{md} % Use normal series for feature texts
+\setshape {features}{it} % Use italics shape for feature texts
+\setsize {features}{normalsize} % Use normal size for feature texts
+\setfamily{legend}{tt} % Use typewriter family for legend texts
+\setseries{legend}{md} % Use normal series for legend texts
+\setshape {legend}{up} % Use upright shape for legend texts
+\setsize {legend}{normalsize} % Use normal size for legend texts
+\tintdefault{medium} % Use medium tint intensity
+\emphdefault{it} % Use italics to emphasize regions
+\showonPHDsec{alpha,beta} % Show helices and strands (PHD input)
+\showonPHDtopo{internal,external,TM}% Show int., ext. and TM's (PHD input)
+\showonHMMTOP{TM} % Show TM's (not int/ext on HMMTOP input)
+\showonSTRIDE{alpha,3-10,pi,beta} % Show helices and strands (STRIDE input)
+\showonDSSP{alpha,3-10,pi,beta} % Show helices and strands (DSSP input)
+\secondcolumnDSSP % Use numbering from 2. column in DSSP
+\appearance{PHDtopo}{internal} % \
+ {bottom}{'-'} % \
+ {int.\ \Alphacount} % |
+\appearance{PHDtopo}{external} % |
+ {top}{,-,} % |
+ {ext.\ \Alphacount} % |
+\appearance{PHDtopo}{TM}{top} % |
+ {box[LightGray]:TM\numcount}{} % |
+\appearance{HMMTOP}{internal} % |
+ {bottom}{---} % |
+ {int.\ \Alphacount} % |
+\appearance{HMMTOP}{external} % |
+ {top}{---} % |
+ {ext.\ \Alphacount} % |
+\appearance{HMMTOP}{TM}{top} % |
+ {helix}{TM\numcount} % |
+\appearance{PHDsec}{alpha}{top} % |
+ {box:$\alpha$\numcount}{} % |
+\appearance{PHDsec}{beta}{top} % |
+ {-->}{$\beta$\numcount} % |
+\appearance{STRIDE}{alpha}{top} % |
+ {box:$\alpha$\numcount}{} % | Definitions for the appearance of
+\appearance{STRIDE}{3-10}{top} % \
+ {fill:$\circ$}{3$_{10}$} % > secondary structures included from|
+\appearance{STRIDE}{pi} % /
+ {top}{---}{$\pi$} % | PHD-, STRIDE-, or DSSP-files.
+\appearance{STRIDE}{beta}{top} % |
+ {-->}{$\beta$\numcount} % |
+\appearance{STRIDE}{bridge} % |
+ {top}{fill:$\uparrow$}{} % |
+\appearance{STRIDE}{turn} % |
+ {top}{,-,}{turn} % |
+\appearance{DSSP}{alpha}{top} % |
+ {box:$\alpha$\numcount}{} % |
+\appearance{DSSP}{3-10}{top} % |
+ {fill:$\circ$}{3$_{10}$} % |
+\appearance{DSSP}{pi} % |
+ {top}{---}{$\pi$} % |
+\appearance{DSSP}{beta}{top} % |
+ {-->}{$\beta$\numcount} % |
+\appearance{DSSP}{bridge} % |
+ {top}{fill:$\uparrow$}{} % |
+\appearance{DSSP}{turn} % |
+ {top}{,-,}{turn} % |
+\appearance{DSSP}{bend}{top} % /
+ {fill:$\diamond$}{} % /
+
+\pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ} % Amino acid grouping due to similarity
+
+\pepsims{F}{YW} % Y and W are similar to F
+\pepsims{Y}{WF} % W and F are similar to Y
+\pepsims{W}{YF} % Y and F are similar to W
+
+\pepsims{I}{LVM} % L, V and M are similar to I
+\pepsims{L}{VMI} % V, M and I are similar to L
+\pepsims{V}{MIL} % M, I and L are similar to V
+
+\pepsims{R}{KH} % K and H are similar to R
+\pepsims{K}{HR} % H and R are similar to K
+\pepsims{H}{RK} % R and K are similar to H
+
+\pepsims{A}{GS} % G and S are similar to A
+\pepsims{G}{A} % A (but not S) is similar to G
+
+\pepsims{S}{TA} % T and A are similar to S
+\pepsims{T}{S} % S (but not A) is similar to T
+
+\pepsims{D}{EN} % E and N (but not Q) are similar to D
+\pepsims{E}{DQ} % D and Q (but not N) are similar to E
+\pepsims{N}{QD} % Q and D (but not E) are similar to N
+\pepsims{Q}{NE} % N and E (but not D) are similar to Q
+
+\DNAgroups{GAR,CTY} % Nucleotide grouping due to similarity
+
+\DNAsims{A}{GR} % G and R are similar to A
+\DNAsims{G}{AR} % A and R are similar to G
+\DNAsims{R}{AG} % A and G are similar to R
+
+\DNAsims{C}{TY} % T and Y are similar to C
+\DNAsims{T}{CY} % C and Y are similar to T
+\DNAsims{Y}{CT} % C and T are similar to Y