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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} % Do not stretch character width
\linestretch{1} % Do not stretch lines vertically
\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{right} % Show sequence numbering on the left
\namescolor{Black} % Names' color is `Black'
\shownames{left} % 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
\hidesequencelogo % Do not show a sequence logo as consensus
\showlogoscale{leftright} % Show vertical scale bar if logo is on
\logostretch{1} % Do not stretch sequence logo vertically
\hidesubfamilylogo % Do not show a subfamily logo
\subfamilythreshold{50} % Set subfamily threshold to 50%
\shownegatives % Show negative values in subfamily logo
\showrelevance[Black]{*} % Label relevant subfamily deviations
\defconsensus{{}}{*}{!} % Blank =no match; * =match; ! =all match
\showleadinggaps % Show gap symbols before sequence start
\rulercolor{Black} % Ruler's color is `Black'
\hideruler % Do not show the ruler
\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
\setfamily{ruler}{sf} % Use sans serif font for ruler numbers
\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
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