texshadow 1.16 (19feb07)

git-svn-id: svn://tug.org/texlive/trunk@3983 c570f23f-e606-0410-a88d-b1316a301751

1 files changed, 695 insertions, 129 deletions

diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty
index 729d15deb04..792807ef473 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.sty
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.sty
@@ -8,13 +8,13 @@
 %% 
 %% LaTeX package for typesetting nucleotide and peptide alignments
 %% 
-%% Copyright (C) 1999-2006 Eric Beitz
+%% Copyright (C) 1999-2007 Eric Beitz
 %% See the file texshade.txt
 %% 
 
 \NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2006/06/27 LaTeX TeXshade (v1.15)]
-\message{Package `texshade', Version 1.15 of 2006/06/27.}
+\ProvidesPackage{texshade}[2007/02/18 LaTeX TeXshade (v1.16)]
+\message{Package `texshade', Version 1.16 of 2007/02/18.}
 
 \PassOptionsToPackage{dvips}{color}
 \PassOptionsToPackage{dvips}{graphicx}
@@ -55,6 +55,7 @@
 
 \newread\structurefile  \newwrite\featurefile
 \newread\alignfile      \newread\sublogofile
+\newwrite\exp@rtfile
 
 \expandafter\ifx\csname blacktriangleright\endcsname\relax
  \openin\structurefile = amssymb.sty
@@ -487,122 +488,184 @@
 \xdef\consCG{50} \xdef\consCN{33} \xdef\consCD{17} \xdef\consCE{0} \xdef\consCQ{17}
 \xdef\consCH{33} \xdef\consCR{33} \xdef\consCK{0} \xdef\consCM{33} \xdef\consCI{33}
 \xdef\consCL{33} \xdef\consCV{33} \xdef\consCF{50} \xdef\consCY{50} \xdef\consCW{50}
+\xdef\consCB{0}  \xdef\consCJ{0}  \xdef\consCO{0}  \xdef\consCU{0}  \xdef\consCX{0}  \xdef\consCZ{0}
 \expandafter\xdef\csname consC.\endcsname{0}
 
 \xdef\consSC{67} \xdef\consSS{100} \xdef\consST{83} \xdef\consSP{67} \xdef\consSA{83}
 \xdef\consSG{83} \xdef\consSN{83} \xdef\consSD{67} \xdef\consSE{50} \xdef\consSQ{50}
 \xdef\consSH{50} \xdef\consSR{50} \xdef\consSK{50} \xdef\consSM{33} \xdef\consSI{33}
 \xdef\consSL{33} \xdef\consSV{67} \xdef\consSF{50} \xdef\consSY{50} \xdef\consSW{33}
+\xdef\consSB{0}  \xdef\consSJ{0}  \xdef\consSO{0}  \xdef\consSU{0}  \xdef\consSX{0}  \xdef\consSZ{0}
 \expandafter\xdef\csname consS.\endcsname{0}
 
 \xdef\consTC{33} \xdef\consTS{83} \xdef\consTT{100} \xdef\consTP{67} \xdef\consTA{83}
 \xdef\consTG{67} \xdef\consTN{67} \xdef\consTD{50} \xdef\consTE{50} \xdef\consTQ{50}
 \xdef\consTH{33} \xdef\consTR{50} \xdef\consTK{67} \xdef\consTM{50} \xdef\consTI{50}
 \xdef\consTL{33} \xdef\consTV{67} \xdef\consTF{33} \xdef\consTY{33} \xdef\consTW{17}
+\xdef\consTB{0}  \xdef\consTJ{0}  \xdef\consTO{0}  \xdef\consTU{0}  \xdef\consTX{0}  \xdef\consTZ{0}
 \expandafter\xdef\csname consT.\endcsname{0}
 
 \xdef\consPC{33} \xdef\consPS{67} \xdef\consPT{67} \xdef\consPP{100} \xdef\consPA{83}
 \xdef\consPG{67} \xdef\consPN{33} \xdef\consPD{50} \xdef\consPE{50} \xdef\consPQ{50}
 \xdef\consPH{50} \xdef\consPR{50} \xdef\consPK{33} \xdef\consPM{33} \xdef\consPI{33}
 \xdef\consPL{50} \xdef\consPV{67} \xdef\consPF{50} \xdef\consPY{33} \xdef\consPW{33}
+\xdef\consPB{0}  \xdef\consPJ{0}  \xdef\consPO{0}  \xdef\consPU{0}  \xdef\consPX{0}  \xdef\consPZ{0}
 \expandafter\xdef\csname consP.\endcsname{0}
 
 \xdef\consAC{33} \xdef\consAS{83} \xdef\consAT{83} \xdef\consAP{83} \xdef\consAA{100}
 \xdef\consAG{83} \xdef\consAN{50} \xdef\consAD{67} \xdef\consAE{67} \xdef\consAQ{50}
 \xdef\consAH{33} \xdef\consAR{33} \xdef\consAK{50} \xdef\consAM{50} \xdef\consAI{33}
 \xdef\consAL{33} \xdef\consAV{83} \xdef\consAF{50} \xdef\consAY{33} \xdef\consAW{33}
+\xdef\consAB{0}  \xdef\consAJ{0}  \xdef\consAO{0}  \xdef\consAU{0}  \xdef\consAX{0}  \xdef\consAZ{0}
 \expandafter\xdef\csname consA.\endcsname{0}
 
 \xdef\consGC{50} \xdef\consGS{83} \xdef\consGT{67} \xdef\consGP{67} \xdef\consGA{83}
 \xdef\consGG{100} \xdef\consGN{50} \xdef\consGD{67} \xdef\consGE{67} \xdef\consGQ{33}
 \xdef\consGH{17} \xdef\consGR{50} \xdef\consGK{33} \xdef\consGM{17} \xdef\consGI{33}
 \xdef\consGL{33} \xdef\consGV{67} \xdef\consGF{33} \xdef\consGY{33} \xdef\consGW{50}
+\xdef\consGB{0}  \xdef\consGJ{0}  \xdef\consGO{0}  \xdef\consGU{0}  \xdef\consGX{0}  \xdef\consGZ{0}
 \expandafter\xdef\csname consG.\endcsname{0}
 
 \xdef\consNC{33} \xdef\consNS{83} \xdef\consNT{67} \xdef\consNP{33} \xdef\consNA{50}
 \xdef\consNG{50} \xdef\consNN{100} \xdef\consND{83} \xdef\consNE{67} \xdef\consNQ{50}
 \xdef\consNH{67} \xdef\consNR{50} \xdef\consNK{67} \xdef\consNM{17} \xdef\consNI{33}
 \xdef\consNL{17} \xdef\consNV{33} \xdef\consNF{33} \xdef\consNY{50} \xdef\consNW{0}
+\xdef\consNB{0}  \xdef\consNJ{0}  \xdef\consNO{0}  \xdef\consNU{0}  \xdef\consNX{0}  \xdef\consNZ{0}
 \expandafter\xdef\csname consN.\endcsname{0}
 
 \xdef\consDC{17} \xdef\consDS{67} \xdef\consDT{50} \xdef\consDP{50} \xdef\consDA{67}
 \xdef\consDG{67} \xdef\consDN{83} \xdef\consDD{100} \xdef\consDE{83} \xdef\consDQ{67}
 \xdef\consDH{50} \xdef\consDR{33} \xdef\consDK{50} \xdef\consDM{33} \xdef\consDI{17}
 \xdef\consDL{17} \xdef\consDV{50} \xdef\consDF{17} \xdef\consDY{33} \xdef\consDW{0}
+\xdef\consDB{0}  \xdef\consDJ{0}  \xdef\consDO{0}  \xdef\consDU{0}  \xdef\consDX{0}  \xdef\consDZ{0}
 \expandafter\xdef\csname consD.\endcsname{0}
 
 \xdef\consEC{0} \xdef\consES{50} \xdef\consET{50} \xdef\consEP{50} \xdef\consEA{67}
 \xdef\consEG{67} \xdef\consEN{67} \xdef\consED{83} \xdef\consEE{100} \xdef\consEQ{67}
 \xdef\consEH{33} \xdef\consER{50} \xdef\consEK{67} \xdef\consEM{33} \xdef\consEI{17}
 \xdef\consEL{17} \xdef\consEV{67} \xdef\consEF{33} \xdef\consEY{17} \xdef\consEW{17}
+\xdef\consEB{0}  \xdef\consEJ{0}  \xdef\consEO{0}  \xdef\consEU{0}  \xdef\consEX{0}  \xdef\consEZ{0}
 \expandafter\xdef\csname consE.\endcsname{0}
 
 \xdef\consQC{17} \xdef\consQS{50} \xdef\consQT{50} \xdef\consQP{50} \xdef\consQA{50}
 \xdef\consQG{33} \xdef\consQN{50} \xdef\consQD{67} \xdef\consQE{67} \xdef\consQQ{100}
 \xdef\consQH{67} \xdef\consQR{50} \xdef\consQK{67} \xdef\consQM{33} \xdef\consQI{17}
 \xdef\consQL{33} \xdef\consQV{33} \xdef\consQF{17} \xdef\consQY{33} \xdef\consQW{17}
+\xdef\consQB{0}  \xdef\consQJ{0}  \xdef\consQO{0}  \xdef\consQU{0}  \xdef\consQX{0}  \xdef\consQZ{0}
 \expandafter\xdef\csname consQ.\endcsname{0}
 
 \xdef\consHC{33} \xdef\consHS{50} \xdef\consHT{33} \xdef\consHP{50} \xdef\consHA{33}
 \xdef\consHG{17} \xdef\consHN{67} \xdef\consHD{50} \xdef\consHE{33} \xdef\consHQ{67}
 \xdef\consHH{100} \xdef\consHR{67} \xdef\consHK{50} \xdef\consHM{33} \xdef\consHI{33}
 \xdef\consHL{50} \xdef\consHV{17} \xdef\consHF{33} \xdef\consHY{50} \xdef\consHW{17}
+\xdef\consHB{0}  \xdef\consHJ{0}  \xdef\consHO{0}  \xdef\consHU{0}  \xdef\consHX{0}  \xdef\consHZ{0}
 \expandafter\xdef\csname consH.\endcsname{0}
 
 \xdef\consRC{33} \xdef\consRS{50} \xdef\consRT{50} \xdef\consRP{50} \xdef\consRA{33}
 \xdef\consRG{50} \xdef\consRN{50} \xdef\consRD{33} \xdef\consRE{50} \xdef\consRQ{50}
 \xdef\consRH{67} \xdef\consRR{100} \xdef\consRK{83} \xdef\consRM{33} \xdef\consRI{33}
 \xdef\consRL{33} \xdef\consRV{33} \xdef\consRF{17} \xdef\consRY{17} \xdef\consRW{33}
+\xdef\consRB{0}  \xdef\consRJ{0}  \xdef\consRO{0}  \xdef\consRU{0}  \xdef\consRX{0}  \xdef\consRZ{0}
 \expandafter\xdef\csname consR.\endcsname{0}
 
 \xdef\consKC{0} \xdef\consKS{50} \xdef\consKT{67} \xdef\consKP{33} \xdef\consKA{50}
 \xdef\consKG{33} \xdef\consKN{67} \xdef\consKD{50} \xdef\consKE{67} \xdef\consKQ{67}
 \xdef\consKH{50} \xdef\consKR{83} \xdef\consKK{100} \xdef\consKM{33} \xdef\consKI{33}
 \xdef\consKL{33} \xdef\consKV{50} \xdef\consKF{17} \xdef\consKY{17} \xdef\consKW{17}
+\xdef\consKB{0}  \xdef\consKJ{0}  \xdef\consKO{0}  \xdef\consKU{0}  \xdef\consKX{0}  \xdef\consKZ{0}
 \expandafter\xdef\csname consK.\endcsname{0}
 
 \xdef\consMC{33} \xdef\consMS{50} \xdef\consMT{50} \xdef\consMP{33} \xdef\consMA{50}
 \xdef\consMG{17} \xdef\consMN{17} \xdef\consMD{33} \xdef\consME{33} \xdef\consMQ{33}
 \xdef\consMH{33} \xdef\consMR{33} \xdef\consMK{33} \xdef\consMM{100} \xdef\consMI{67}
 \xdef\consML{83} \xdef\consMV{67} \xdef\consMF{50} \xdef\consMY{33} \xdef\consMW{50}
+\xdef\consMB{0}  \xdef\consMJ{0}  \xdef\consMO{0}  \xdef\consMU{0}  \xdef\consMX{0}  \xdef\consMZ{0}
 \expandafter\xdef\csname consM.\endcsname{0}
 
 \xdef\consIC{33} \xdef\consIS{33} \xdef\consIT{50} \xdef\consIP{33} \xdef\consIA{33}
 \xdef\consIG{33} \xdef\consIN{33} \xdef\consID{17} \xdef\consIE{17} \xdef\consIQ{17}
 \xdef\consIH{33} \xdef\consIR{33} \xdef\consIK{33} \xdef\consIM{67} \xdef\consII{100}
 \xdef\consIL{83} \xdef\consIV{33} \xdef\consIF{67} \xdef\consIY{50} \xdef\consIW{50}
+\xdef\consIB{0}  \xdef\consIJ{0}  \xdef\consIO{0}  \xdef\consIU{0}  \xdef\consIX{0}  \xdef\consIZ{0}
 \expandafter\xdef\csname consI.\endcsname{0}
 
 \xdef\consLC{33} \xdef\consLS{33} \xdef\consLT{33} \xdef\consLP{50} \xdef\consLA{33}
 \xdef\consLG{33} \xdef\consLN{17} \xdef\consLD{17} \xdef\consLE{17} \xdef\consLQ{33}
 \xdef\consLH{50} \xdef\consLR{33} \xdef\consLK{33} \xdef\consLM{83} \xdef\consLI{83}
 \xdef\consLL{100} \xdef\consLV{33} \xdef\consLF{67} \xdef\consLY{50} \xdef\consLW{67}
+\xdef\consLB{0}  \xdef\consLJ{0}  \xdef\consLO{0}  \xdef\consLU{0}  \xdef\consLX{0}  \xdef\consLZ{0}
 \expandafter\xdef\csname consL.\endcsname{0}
 
 \xdef\consVC{33} \xdef\consVS{67} \xdef\consVT{67} \xdef\consVP{67} \xdef\consVA{83}
 \xdef\consVG{67} \xdef\consVN{33} \xdef\consVD{50} \xdef\consVE{67} \xdef\consVQ{33}
 \xdef\consVH{17} \xdef\consVR{33} \xdef\consVK{50} \xdef\consVM{67} \xdef\consVI{33}
 \xdef\consVL{33} \xdef\consVV{100} \xdef\consVF{67} \xdef\consVY{50} \xdef\consVW{50}
+\xdef\consVB{0}  \xdef\consVJ{0}  \xdef\consVO{0}  \xdef\consVU{0}  \xdef\consVX{0}  \xdef\consVZ{0}
 \expandafter\xdef\csname consV.\endcsname{0}
 
 \xdef\consFC{50} \xdef\consFS{50} \xdef\consFT{33} \xdef\consFP{50} \xdef\consFA{50}
 \xdef\consFG{33} \xdef\consFN{33} \xdef\consFD{17} \xdef\consFE{33} \xdef\consFQ{17}
 \xdef\consFH{33} \xdef\consFR{17} \xdef\consFK{17} \xdef\consFM{50} \xdef\consFI{67}
 \xdef\consFL{67} \xdef\consFV{67} \xdef\consFF{100} \xdef\consFY{83} \xdef\consFW{50}
+\xdef\consFB{0}  \xdef\consFJ{0}  \xdef\consFO{0}  \xdef\consFU{0}  \xdef\consFX{0}  \xdef\consFZ{0}
 \expandafter\xdef\csname consF.\endcsname{0}
 
 \xdef\consYC{50} \xdef\consYS{50} \xdef\consYT{33} \xdef\consYP{33} \xdef\consYA{33}
 \xdef\consYG{33} \xdef\consYN{50} \xdef\consYD{33} \xdef\consYE{17} \xdef\consYQ{33}
 \xdef\consYH{50} \xdef\consYR{17} \xdef\consYK{17} \xdef\consYM{33} \xdef\consYI{50}
 \xdef\consYL{50} \xdef\consYV{50} \xdef\consYF{83} \xdef\consYY{100} \xdef\consYW{50}
+\xdef\consYB{0}  \xdef\consYJ{0}  \xdef\consYO{0}  \xdef\consYU{0}  \xdef\consYX{0}  \xdef\consYZ{0}
 \expandafter\xdef\csname consY.\endcsname{0}
 
 \xdef\consWC{50} \xdef\consWS{33} \xdef\consWT{17} \xdef\consWP{33} \xdef\consWA{33}
 \xdef\consWG{50} \xdef\consWN{0} \xdef\consWD{0} \xdef\consWE{17} \xdef\consWQ{17}
 \xdef\consWH{17} \xdef\consWR{33} \xdef\consWK{17} \xdef\consWM{50} \xdef\consWI{50}
 \xdef\consWL{67} \xdef\consWV{50} \xdef\consWF{50} \xdef\consWY{50} \xdef\consWW{100}
+\xdef\consWB{0}  \xdef\consWJ{0}  \xdef\consWO{0}  \xdef\consWU{0}  \xdef\consWX{0}  \xdef\consWZ{0}
 \expandafter\xdef\csname consW.\endcsname{0}
 
+\xdef\consBC{0} \xdef\consBS{0} \xdef\consBT{0} \xdef\consBP{0} \xdef\consBA{0}
+\xdef\consBG{0} \xdef\consBN{0} \xdef\consBD{0} \xdef\consBE{0} \xdef\consBQ{0}
+\xdef\consBH{0} \xdef\consBR{0} \xdef\consBK{0} \xdef\consBM{0} \xdef\consBI{0}
+\xdef\consBL{0} \xdef\consBV{0} \xdef\consBF{0} \xdef\consBY{0} \xdef\consBW{0}
+\xdef\consBB{100} \xdef\consBJ{0} \xdef\consBO{0} \xdef\consBU{0}  \xdef\consBX{0}  \xdef\consBZ{0}
+\expandafter\xdef\csname consB.\endcsname{0}
+
+\xdef\consJC{0} \xdef\consJS{0} \xdef\consJT{0} \xdef\consJP{0} \xdef\consJA{0}
+\xdef\consJG{0} \xdef\consJN{0} \xdef\consJD{0} \xdef\consJE{0} \xdef\consJQ{0}
+\xdef\consJH{0} \xdef\consJR{0} \xdef\consJK{0} \xdef\consJM{0} \xdef\consJI{0}
+\xdef\consJL{0} \xdef\consJV{0} \xdef\consJF{0} \xdef\consJY{0} \xdef\consJW{0}
+\xdef\consJB{0} \xdef\consJJ{100} \xdef\consJO{0} \xdef\consJU{0}  \xdef\consJX{0}  \xdef\consJZ{0}
+\expandafter\xdef\csname consJ.\endcsname{0}
+
+\xdef\consOC{0} \xdef\consOS{0} \xdef\consOT{0} \xdef\consOP{0} \xdef\consOA{0}
+\xdef\consOG{0} \xdef\consON{0} \xdef\consOD{0} \xdef\consOE{0} \xdef\consOQ{0}
+\xdef\consOH{0} \xdef\consOR{0} \xdef\consOK{0} \xdef\consOM{0} \xdef\consOI{0}
+\xdef\consOL{0} \xdef\consOV{0} \xdef\consOF{0} \xdef\consOY{0} \xdef\consOW{0}
+\xdef\consOB{0} \xdef\consOJ{0} \xdef\consOO{100} \xdef\consOU{0}  \xdef\consOX{0}  \xdef\consOZ{0}
+\expandafter\xdef\csname consO.\endcsname{0}
+
+\xdef\consUC{0} \xdef\consUS{0} \xdef\consUT{0} \xdef\consUP{0} \xdef\consUA{0}
+\xdef\consUG{0} \xdef\consUN{0} \xdef\consUD{0} \xdef\consUE{0} \xdef\consUQ{0}
+\xdef\consUH{0} \xdef\consUR{0} \xdef\consUK{0} \xdef\consUM{0} \xdef\consUI{0}
+\xdef\consUL{0} \xdef\consUV{0} \xdef\consUF{0} \xdef\consUY{0} \xdef\consUW{0}
+\xdef\consUB{0} \xdef\consUJ{0} \xdef\consUO{0} \xdef\consUU{100}  \xdef\consUX{0}  \xdef\consUZ{0}
+\expandafter\xdef\csname consU.\endcsname{0}
+
+\xdef\consXC{0} \xdef\consXS{0} \xdef\consXT{0} \xdef\consXP{0} \xdef\consXA{0}
+\xdef\consXG{0} \xdef\consXN{0} \xdef\consXD{0} \xdef\consXE{0} \xdef\consXQ{0}
+\xdef\consXH{0} \xdef\consXR{0} \xdef\consXK{0} \xdef\consXM{0} \xdef\consXI{0}
+\xdef\consXL{0} \xdef\consXV{0} \xdef\consXF{0} \xdef\consXY{0} \xdef\consXW{0}
+\xdef\consXB{0} \xdef\consXJ{0} \xdef\consXO{0} \xdef\consXU{0}  \xdef\consXX{100}  \xdef\consXZ{0}
+\expandafter\xdef\csname consX.\endcsname{0}
+
+\xdef\consZC{0} \xdef\consZS{0} \xdef\consZT{0} \xdef\consZP{0} \xdef\consZA{0}
+\xdef\consZG{0} \xdef\consZN{0} \xdef\consZD{0} \xdef\consZE{0} \xdef\consZQ{0}
+\xdef\consZH{0} \xdef\consZR{0} \xdef\consZK{0} \xdef\consZM{0} \xdef\consZI{0}
+\xdef\consZL{0} \xdef\consZV{0} \xdef\consZF{0} \xdef\consZY{0} \xdef\consZW{0}
+\xdef\consZB{0} \xdef\consZJ{0} \xdef\consZO{0} \xdef\consZU{0}  \xdef\consZX{0}  \xdef\consZZ{100}
+\expandafter\xdef\csname consZ.\endcsname{0}
+
 \expandafter\xdef\csname cons.C\endcsname{0}
 \expandafter\xdef\csname cons.S\endcsname{0}
 \expandafter\xdef\csname cons.T\endcsname{0}
@@ -623,6 +686,12 @@
 \expandafter\xdef\csname cons.F\endcsname{0}
 \expandafter\xdef\csname cons.Y\endcsname{0}
 \expandafter\xdef\csname cons.W\endcsname{0}
+\expandafter\xdef\csname cons.B\endcsname{0}
+\expandafter\xdef\csname cons.J\endcsname{0}
+\expandafter\xdef\csname cons.O\endcsname{0}
+\expandafter\xdef\csname cons.U\endcsname{0}
+\expandafter\xdef\csname cons.X\endcsname{0}
+\expandafter\xdef\csname cons.Z\endcsname{0}
 \expandafter\xdef\csname cons..\endcsname{0}
 
 \def\c@d@ns{%
@@ -1141,6 +1210,126 @@
 \definecolor{HotCold15}          {rgb} {1,0.40,0}
 \definecolor{HotCold10}          {rgb} {1,0.20,0}
 \definecolor{HotCold5}           {rgb} {0.91,0,0}
+\expandafter\def\csname BlueRed5\endcsname{[0.15,0.17,0.55]}
+\expandafter\def\csname BlueRed10\endcsname{[0.20,0.23,0.57]}
+\expandafter\def\csname BlueRed15\endcsname{[0.24,0.29,0.60]}
+\expandafter\def\csname BlueRed20\endcsname{[0.33,0.35,0.64]}
+\expandafter\def\csname BlueRed25\endcsname{[0.43,0.43,0.68]}
+\expandafter\def\csname BlueRed30\endcsname{[0.52,0.52,0.73]}
+\expandafter\def\csname BlueRed35\endcsname{[0.60,0.60,0.78]}
+\expandafter\def\csname BlueRed40\endcsname{[0.70,0.70,0.84]}
+\expandafter\def\csname BlueRed45\endcsname{[0.80,0.80,0.85]}
+\expandafter\def\csname BlueRed50\endcsname{[0.86,0.82,0.82]}
+\expandafter\def\csname BlueRed55\endcsname{[0.87,0.73,0.73]}
+\expandafter\def\csname BlueRed60\endcsname{[0.89,0.64,0.64]}
+\expandafter\def\csname BlueRed65\endcsname{[0.90,0.55,0.55]}
+\expandafter\def\csname BlueRed70\endcsname{[0.91,0.47,0.46]}
+\expandafter\def\csname BlueRed75\endcsname{[0.91,0.39,0.37]}
+\expandafter\def\csname BlueRed80\endcsname{[0.90,0.33,0.28]}
+\expandafter\def\csname BlueRed85\endcsname{[0.89,0.25,0.20]}
+\expandafter\def\csname BlueRed90\endcsname{[0.88,0.23,0.14]}
+\expandafter\def\csname BlueRed95\endcsname{[0.87,0.21,0.09]}
+\expandafter\def\csname BlueRed100\endcsname{[0.87,0.16,0.04]}
+\expandafter\def\csname RedBlue100\endcsname{[0.15,0.17,0.55]}
+\expandafter\def\csname RedBlue95\endcsname{[0.15,0.17,0.55]}
+\expandafter\def\csname RedBlue90\endcsname{[0.20,0.23,0.57]}
+\expandafter\def\csname RedBlue85\endcsname{[0.24,0.29,0.60]}
+\expandafter\def\csname RedBlue80\endcsname{[0.33,0.35,0.64]}
+\expandafter\def\csname RedBlue75\endcsname{[0.43,0.43,0.68]}
+\expandafter\def\csname RedBlue70\endcsname{[0.52,0.52,0.73]}
+\expandafter\def\csname RedBlue65\endcsname{[0.60,0.60,0.78]}
+\expandafter\def\csname RedBlue60\endcsname{[0.70,0.70,0.84]}
+\expandafter\def\csname RedBlue55\endcsname{[0.80,0.80,0.85]}
+\expandafter\def\csname RedBlue50\endcsname{[0.86,0.82,0.82]}
+\expandafter\def\csname RedBlue45\endcsname{[0.87,0.73,0.73]}
+\expandafter\def\csname RedBlue40\endcsname{[0.89,0.64,0.64]}
+\expandafter\def\csname RedBlue35\endcsname{[0.90,0.55,0.55]}
+\expandafter\def\csname RedBlue30\endcsname{[0.91,0.47,0.46]}
+\expandafter\def\csname RedBlue25\endcsname{[0.91,0.39,0.37]}
+\expandafter\def\csname RedBlue20\endcsname{[0.90,0.33,0.28]}
+\expandafter\def\csname RedBlue15\endcsname{[0.89,0.25,0.20]}
+\expandafter\def\csname RedBlue10\endcsname{[0.88,0.23,0.14]}
+\expandafter\def\csname RedBlue5\endcsname{[0.87,0.21,0.09]}
+\expandafter\def\csname GreenRed5\endcsname{[0,1,0]}
+\expandafter\def\csname GreenRed10\endcsname{[0.05,0.95,0]}
+\expandafter\def\csname GreenRed15\endcsname{[0.10,0.90,0]}
+\expandafter\def\csname GreenRed20\endcsname{[0.15,0.85,0]}
+\expandafter\def\csname GreenRed25\endcsname{[0.20,0.80,0]}
+\expandafter\def\csname GreenRed30\endcsname{[0.25,0.75,0]}
+\expandafter\def\csname GreenRed35\endcsname{[0.30,0.70,0]}
+\expandafter\def\csname GreenRed40\endcsname{[0.35,0.65,0]}
+\expandafter\def\csname GreenRed45\endcsname{[0.40,0.60,0]}
+\expandafter\def\csname GreenRed50\endcsname{[0.45,0.55,0]}
+\expandafter\def\csname GreenRed55\endcsname{[0.50,0.50,0]}
+\expandafter\def\csname GreenRed60\endcsname{[0.55,0.45,0]}
+\expandafter\def\csname GreenRed65\endcsname{[0.60,0.40,0]}
+\expandafter\def\csname GreenRed70\endcsname{[0.65,0.35,0]}
+\expandafter\def\csname GreenRed75\endcsname{[0.70,0.30,0]}
+\expandafter\def\csname GreenRed80\endcsname{[0.75,0.25,0]}
+\expandafter\def\csname GreenRed85\endcsname{[0.80,0.20,0]}
+\expandafter\def\csname GreenRed90\endcsname{[0.85,0.15,0]}
+\expandafter\def\csname GreenRed95\endcsname{[0.90,0.10,0]}
+\expandafter\def\csname GreenRed100\endcsname{[0.95,0.05,0]}
+\expandafter\def\csname RedGreen100\endcsname{[0.05,0.95,0]}
+\expandafter\def\csname RedGreen95\endcsname{[0.10,0.90,0]}
+\expandafter\def\csname RedGreen90\endcsname{[0.15,0.85,0]}
+\expandafter\def\csname RedGreen85\endcsname{[0.20,0.80,0]}
+\expandafter\def\csname RedGreen80\endcsname{[0.25,0.75,0]}
+\expandafter\def\csname RedGreen75\endcsname{[0.30,0.70,0]}
+\expandafter\def\csname RedGreen70\endcsname{[0.35,0.65,0]}
+\expandafter\def\csname RedGreen65\endcsname{[0.40,0.60,0]}
+\expandafter\def\csname RedGreen60\endcsname{[0.45,0.55,0]}
+\expandafter\def\csname RedGreen55\endcsname{[0.50,0.50,0]}
+\expandafter\def\csname RedGreen50\endcsname{[0.55,0.45,0]}
+\expandafter\def\csname RedGreen45\endcsname{[0.60,0.40,0]}
+\expandafter\def\csname RedGreen40\endcsname{[0.65,0.35,0]}
+\expandafter\def\csname RedGreen35\endcsname{[0.70,0.30,0]}
+\expandafter\def\csname RedGreen30\endcsname{[0.75,0.25,0]}
+\expandafter\def\csname RedGreen25\endcsname{[0.80,0.20,0]}
+\expandafter\def\csname RedGreen20\endcsname{[0.85,0.15,0]}
+\expandafter\def\csname RedGreen15\endcsname{[0.90,0.10,0]}
+\expandafter\def\csname RedGreen10\endcsname{[0.95,0.05,0]}
+\expandafter\def\csname RedGreen5\endcsname{[1,0,0]}
+\expandafter\def\csname ColdHot5\endcsname{[0,0.08,1]}
+\expandafter\def\csname ColdHot10\endcsname{[0,0.29,1]}
+\expandafter\def\csname ColdHot15\endcsname{[0,0.49,1]}
+\expandafter\def\csname ColdHot20\endcsname{[0,0.70,1]}
+\expandafter\def\csname ColdHot25\endcsname{[0,0.90,1]}
+\expandafter\def\csname ColdHot30\endcsname{[0,1,0.87]}
+\expandafter\def\csname ColdHot35\endcsname{[0,1,0.68]}
+\expandafter\def\csname ColdHot40\endcsname{[0,1,0.46]}
+\expandafter\def\csname ColdHot45\endcsname{[0,1,0.25]}
+\expandafter\def\csname ColdHot50\endcsname{[0,1,0.04]}
+\expandafter\def\csname ColdHot55\endcsname{[0.16,1,0]}
+\expandafter\def\csname ColdHot60\endcsname{[0.35,1,0]}
+\expandafter\def\csname ColdHot65\endcsname{[0.56,1,0]}
+\expandafter\def\csname ColdHot70\endcsname{[0.79,1,0]}
+\expandafter\def\csname ColdHot75\endcsname{[0.98,1,0]}
+\expandafter\def\csname ColdHot80\endcsname{[1,0.82,0]}
+\expandafter\def\csname ColdHot85\endcsname{[1,0.60,0]}
+\expandafter\def\csname ColdHot90\endcsname{[1,0.40,0]}
+\expandafter\def\csname ColdHot95\endcsname{[1,0.20,0]}
+\expandafter\def\csname ColdHot100\endcsname{[0.91,0,0]}
+\expandafter\def\csname HotCold100\endcsname{[0,0.08,1]}
+\expandafter\def\csname HotCold95\endcsname{[0,0.29,1]}
+\expandafter\def\csname HotCold90\endcsname{[0,0.49,1]}
+\expandafter\def\csname HotCold85\endcsname{[0,0.70,1]}
+\expandafter\def\csname HotCold80\endcsname{[0,0.90,1]}
+\expandafter\def\csname HotCold75\endcsname{[0,1,0.87]}
+\expandafter\def\csname HotCold70\endcsname{[0,1,0.68]}
+\expandafter\def\csname HotCold65\endcsname{[0,1,0.46]}
+\expandafter\def\csname HotCold60\endcsname{[0,1,0.25]}
+\expandafter\def\csname HotCold55\endcsname{[0,1,0.04]}
+\expandafter\def\csname HotCold50\endcsname{[0.16,1,0]}
+\expandafter\def\csname HotCold45\endcsname{[0.35,1,0]}
+\expandafter\def\csname HotCold40\endcsname{[0.56,1,0]}
+\expandafter\def\csname HotCold35\endcsname{[0.79,1,0]}
+\expandafter\def\csname HotCold30\endcsname{[0.98,1,0]}
+\expandafter\def\csname HotCold25\endcsname{[1,0.82,0]}
+\expandafter\def\csname HotCold20\endcsname{[1,0.60,0]}
+\expandafter\def\csname HotCold15\endcsname{[1,0.40,0]}
+\expandafter\def\csname HotCold10\endcsname{[1,0.20,0]}
+\expandafter\def\csname HotCold5\endcsname{[0.91,0,0]}
 
 \def\make@lower{%
 \if\first@ A\xdef\first@{a}\else \if\first@ B\xdef\first@{b}\else
@@ -1256,6 +1445,8 @@
                     \csname stack@@reg#1\endcsname}
       \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{%
                     \csname stack@@tintreg#1\endcsname}
+      \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{%
+                    \csname stack@@hidereg#1\endcsname}
       \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{%
                     \csname stack@@emphreg#1\endcsname}
       \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
@@ -1299,6 +1490,8 @@
             \csname stack@reg\the\loopcount\endcsname}
          \expandafter\xdef\csname stack@@tintreg\the\loopcount\endcsname{%
             \csname stack@tintreg\the\loopcount\endcsname}
+         \expandafter\xdef\csname stack@@hidereg\the\loopcount\endcsname{%
+            \csname stack@hidereg\the\loopcount\endcsname}
          \expandafter\xdef\csname stack@@emphreg\the\loopcount\endcsname{%
             \csname stack@emphreg\the\loopcount\endcsname}
          \expandafter\xdef\csname stack@@framereg\the\loopcount\endcsname{%
@@ -1576,6 +1769,8 @@
             \csname stack@reg\the\innerloopcount\endcsname}
       \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{%
             \csname stack@tintreg\the\innerloopcount\endcsname}
+      \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{%
+            \csname stack@hidereg\the\innerloopcount\endcsname}
       \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{%
             \csname stack@emphreg\the\innerloopcount\endcsname}
       \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
@@ -1855,6 +2050,36 @@
    \sort@stack
    \expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack}
 }
+\def\getregion@fromhidestack#1{%
+   \xdef\temp@{#1}
+   \xdef\first@{\csname stack@hidereg\temp@\endcsname}
+   \expandafter\get@fromstack\first@
+   \expandafter\xdef\csname hidestart\temp@\endcsname{\first@}
+   \expandafter\xdef\csname hidestop\temp@\endcsname{\second@}
+   \expandafter\xdef\csname hidestyle\temp@\endcsname{\third@}
+   \expandafter\xdef\csname hidetext\temp@\endcsname{\fourth@}
+   \expandafter\xdef\csname stack@hidereg\temp@\endcsname{\last@}
+}
+\def\sort@hidestack{%
+   \expandafter\get@fromstack\last@
+   \ifx\first@\ampers@nd
+      \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\text@;&;&;&;&;&;@}
+   \else
+   \ifnum\st@rt<\second@
+      \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\text@;%
+                     \first@;\second@;\third@;\fourth@;\last@}
+   \else
+      \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@hidestack
+   \fi\fi
+}
+\def\get@hideregions#1..#2,#3@{%
+   \xdef\hide@true{y}
+   \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
+   \xdef\last@{\csname stack@hidereg\seq@\endcsname}
+   \xdef\tmpstack{}
+   \sort@hidestack
+   \expandafter\xdef\csname stack@hidereg\seq@\endcsname{\tmpstack}
+}
 \def\get@fromemphstack#1;#2;#3;#4@{%
    \xdef\first@{#1} \xdef\second@{#2}
    \xdef\third@{#3} \xdef\last@{#4@}
@@ -1969,6 +2194,14 @@
    \sort@fstack
    \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack}
 }
+\def\get@frameregions#1..#2,#3@{%
+   \frame@true
+   \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
+   \xdef\last@{\csname stack@framereg\seq@\endcsname}
+   \xdef\tmpstack{}
+   \sort@emphstack
+   \expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack}
+}
 \def\getarrow@shape#1#2#3#4&{%
    \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}
    \if\first@@ v
@@ -3334,6 +3567,23 @@
      \ifx\list@\ampers@nd\else\repeat
    \fi
 }
+\def\hideblock#1#2#3#4{%
+   \xdef\seq@{#1}
+   \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
+   \xdef\first@{\seq@ @} \expandafter\check@letter\first@
+   \xdef\first@{\seq@}
+   \ifletter \get@name@number \xdef\seq@{\first@} \fi
+   \ifnum\seq@>\seq@count
+     \message{<Ignored seq `\seq@' in \noexpand\hideblock>}
+   \else
+     \xdef\@ll{#3} \xdef\text@{#4}
+     \xdef\list@{#2,&}
+     \loop
+        \xdef\list@{\list@ @}
+        \expandafter\get@hideregions\list@
+     \ifx\list@\ampers@nd\else\repeat
+   \fi
+}
 \def\bargraphstretch#1{\def\b@r@stretch{#1}}
 \def\colorscalestretch#1{\def\sc@le@stretch{#1}}
 \def\rm@@measure#1#2@{%
@@ -3874,7 +4124,8 @@
       \ifnum\last@<1 \xdef\last@{1}\fi
       \simmodetrue  \funcmodefalse
       \threshold{0}
-      \donotshade{\last@} \constosingleseq{\last@}
+      \xdef\divref@{\last@}
+      \constosingleseq{\last@}
       \nomatchresidues{Black}{White}{lower}{up}
       \similarresidues{Black}{White}{lower}{up}
       \conservedresidues{Black}{White}{{.}}{up}
@@ -4289,6 +4540,9 @@
 }
 \def\rotateruler{\xdef\ruler@rot{90}}
 \def\unrotateruler{\xdef\ruler@rot{0}}
+\def\namerulerpos#1#2{%
+   \expandafter\xdef\csname alt@ruler#1\endcsname{#2}
+}
 \def\featurerule#1{\setlength\rule@thick{#1}}
 \def\orderseqs#1{%
    \def\order@loop{%
@@ -4353,6 +4607,9 @@
    \xdef\temp@{legend}
    \ifx\first@\temp@ \xdef\legend@family{\third@}
    \else
+   \xdef\temp@{hideblock}
+   \ifx\first@\temp@ \xdef\hideblock@family{\third@}
+   \else
    \xdef\temp@{labels}
    \ifx\first@\temp@ \xdef\label@family{\third@}
    \else
@@ -4368,8 +4625,9 @@
       \xdef\residues@family{\third@}
       \xdef\legend@family{\third@}
       \xdef\label@family{\third@}
+      \xdef\hideblock@family{\third@}
       \xdef\ruler@family{\second@}
-   \fi\fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
    \fi
 }
 \def\setseries#1#2{%
@@ -4406,6 +4664,9 @@
    \xdef\temp@{legend}
    \ifx\first@\temp@ \xdef\legend@series{\third@}
    \else
+   \xdef\temp@{hideblock}
+   \ifx\first@\temp@ \xdef\hideblock@series{\third@}
+   \else
    \xdef\temp@{labels}
    \ifx\first@\temp@ \xdef\label@series{\third@}
    \else
@@ -4417,8 +4678,9 @@
       \xdef\namestext@series{\third@}
       \xdef\residues@series{\third@}
       \xdef\legend@series{\third@}
+      \xdef\hideblock@series{\third@}
       \xdef\label@series{\third@}
-   \fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi
    \fi
 }
 \def\setshape#1#2{%
@@ -4463,6 +4725,9 @@
    \xdef\temp@{legend}
    \ifx\first@\temp@ \xdef\legend@shape{\third@}
    \else
+   \xdef\temp@{hideblock}
+   \ifx\first@\temp@ \xdef\hideblock@shape{\third@}
+   \else
    \xdef\temp@{labels}
    \ifx\first@\temp@ \xdef\label@shape{\third@}
    \else
@@ -4474,8 +4739,9 @@
       \xdef\namestext@shape{\third@}
       \xdef\residues@shape{\third@}
       \xdef\legend@shape{\third@}
+      \xdef\hideblock@shape{\third@}
       \xdef\label@shape{\third@}
-   \fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi
    \fi
 }
 \def\setsize#1#2{%
@@ -4503,6 +4769,20 @@
    \ifx\first@\temp@
       \def\legend@size{\csname #2\endcsname}
    \else
+   \xdef\temp@{hideblock}
+   \ifx\first@\temp@
+      \xdef\temp@@{#2}
+      \xdef\temp@{huge}
+      \ifx\temp@\temp@@
+         \def\hideblock@size{\csname LARGE\endcsname}
+      \else
+      \xdef\temp@{Huge}
+      \ifx\temp@\temp@@
+         \def\hideblock@size{\csname LARGE\endcsname}
+      \else
+         \def\hideblock@size{\csname #2\endcsname}
+      \fi\fi
+   \else
    \xdef\temp@{labels}
    \ifx\first@\temp@
       \def\label@size{\csname #2\endcsname}
@@ -4519,10 +4799,11 @@
       \def\numbertext@size{\csname #2\endcsname}
       \def\namestext@size{\csname #2\endcsname}
       \def\legend@size{\csname #2\endcsname}
+      \def\hideblock@size{\csname #2\endcsname}
       \def\label@size{\csname #2\endcsname}
       \def\residues@size{\csname #2\endcsname}
       \xdef\res@size{#2}
-   \fi\fi\fi\fi\fi\fi\fi\fi
+   \fi\fi\fi\fi\fi\fi\fi\fi\fi
    \xdef\temp@{Huge}
    \ifx\temp@\res@size
       \def\bottomruler@size{\csname Large\endcsname}
@@ -4668,6 +4949,25 @@
 \def\legendLARGE       {\setsize{legend}{LARGE}}
 \def\legendhuge        {\setsize{legend}{huge}}
 \def\legendHuge        {\setsize{legend}{Huge}}
+\def\hideblockrm{\setfamily{hideblock}{rm}}
+\def\hideblocksf{\setfamily{hideblock}{sf}}
+\def\hideblocktt{\setfamily{hideblock}{tt}}
+\def\hideblockmd{\setseries{hideblock}{md}}
+\def\hideblockbf{\setseries{hideblock}{bf}}
+\def\hideblockup{\setshape {hideblock}{up}}
+\def\hideblockit{\setshape {hideblock}{it}}
+\def\hideblocksl{\setshape {hideblock}{sl}}
+\def\hideblocksc{\setshape {hideblock}{sc}}
+\def\hideblocktiny        {\setsize{hideblock}{tiny}}
+\def\hideblockscriptsize  {\setsize{hideblock}{scriptsize}}
+\def\hideblockfootnotesize{\setsize{hideblock}{footnotesize}}
+\def\hideblocksmall       {\setsize{hideblock}{small}}
+\def\hideblocknormalsize  {\setsize{hideblock}{normalsize}}
+\def\hideblocklarge       {\setsize{hideblock}{large}}
+\def\hideblockLarge       {\setsize{hideblock}{Large}}
+\def\hideblockLARGE       {\setsize{hideblock}{LARGE}}
+\def\hideblockhuge        {\setsize{hideblock}{LARGE}}
+\def\hideblockHuge        {\setsize{hideblock}{LARGE}}
 \def\rulerrm{\setfamily{ruler}{rm}}
 \def\rulersf{\setfamily{ruler}{sf}}
 \def\rulertt{\setfamily{ruler}{tt}}
@@ -5189,6 +5489,16 @@
    \ifx\temp@\first@ \xdef\tr@nstextstyle{4}\fi
 }
 
+\newcommand\exportconsensus[2][export.txt]{%
+   \ifx\exp@rt\n@
+      \xdef\first@{#2 @} \expandafter\check@letter\first@
+      \xdef\first@{#2}   \ifletter \get@name@number \fi
+      \xdef\exp@rt@num{\first@}
+      \xdef\exp@rt{y}
+      \immediate\openout\exp@rtfile = #1
+   \fi
+}
+
 %%%%%  Calculate consensus
 
 \def\check@sim{%
@@ -5379,9 +5689,10 @@
              \expandafter\xdef\csname seq\the\loopcount\endcsname{%
                 \csname seq\the\loopcount\endcsname\third@\first@}
            \else
+             \ifnum\divref@=\loopcount\else
              \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
              \xdef\low@up{upper} \ifx\resn@m@tch\low@up
-             \else \xdef\first@{\resn@m@tch} \fi\fi
+             \else \xdef\first@{\resn@m@tch} \fi\fi\fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -5434,9 +5745,10 @@
           \xdef\last@{\csname res\the\loopcount\endcsname}
           \expandafter\ifnum\csname \prefix@ grp\last@\endcsname=\second@
               \xdef\third@{2}
+              \ifnum\divref@=\loopcount\else
               \xdef\low@up{lower} \ifx\ressimm@tch\low@up \make@lower \else
               \xdef\low@up{upper} \ifx\ressimm@tch\low@up
-              \else \xdef\first@{\ressimm@tch} \fi\fi
+              \else \xdef\first@{\ressimm@tch} \fi\fi\fi
           \else
               \ifx\first@\d@t
                  \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
@@ -5460,9 +5772,10 @@
                  \fi
               \else
                  \xdef\third@{3}
+                 \ifnum\divref@=\loopcount\else
                  \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
                  \xdef\low@up{upper} \ifx\resn@m@tch\low@up
-                 \else \xdef\first@{\resn@m@tch} \fi\fi
+                 \else \xdef\first@{\resn@m@tch} \fi\fi\fi
               \fi
           \fi
           \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
@@ -5584,9 +5897,10 @@
            \expandafter\xdef\csname seq\the\loopcount\endcsname{%
               \csname seq\the\loopcount\endcsname\third@\first@}
          \else
+           \ifnum\divref@=\loopcount\else
            \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
            \xdef\low@up{upper} \ifx\resn@m@tch\low@up
-           \else \xdef\first@{\resn@m@tch} \fi\fi
+           \else \xdef\first@{\resn@m@tch} \fi\fi\fi
            \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                    \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                    \xdef\first@{=\first@}\fi
@@ -5643,17 +5957,20 @@
     \fi
     \xdef\first@{\csname res\the\loopcount\endcsname}
     \ifcase\third@ \or
+    \ifnum\divref@=\loopcount\else
     \xdef\low@up{lower} \ifx\resm@tch\low@up \make@lower \else
     \xdef\low@up{upper} \ifx\resm@tch\low@up
-    \else \xdef\first@{\resm@tch} \fi\fi
+    \else \xdef\first@{\resm@tch} \fi\fi\fi
     \or
+    \ifnum\divref@=\loopcount\else
     \xdef\low@up{lower} \ifx\ressimm@tch\low@up \make@lower \else
     \xdef\low@up{upper} \ifx\ressimm@tch\low@up
-    \else \xdef\first@{\ressimm@tch} \fi\fi
+    \else \xdef\first@{\ressimm@tch} \fi\fi\fi
     \else
+    \ifnum\divref@=\loopcount\else
     \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
     \xdef\low@up{upper} \ifx\resn@m@tch\low@up
-    \else \xdef\first@{\resn@m@tch} \fi\fi
+    \else \xdef\first@{\resn@m@tch} \fi\fi\fi
     \fi
     \ifx\first@\d@t
             \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
@@ -5718,9 +6035,10 @@
                 3\first@}
     \else
     \xdef\first@{\csname res\the\loopcount\endcsname}
+    \ifnum\divref@=\loopcount\else
     \xdef\low@up{lower} \ifx\res@llm@tch\low@up \make@lower \else
     \xdef\low@up{upper} \ifx\res@llm@tch\low@up
-    \else \xdef\first@{\res@llm@tch} \fi\fi
+    \else \xdef\first@{\res@llm@tch} \fi\fi\fi
     \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -5907,6 +6225,7 @@
             \fi
          \fi\fi
       \ifnum\loopcount<\seq@count \repeat
+      \ifx\hide@now\n@
       \loopcount=0
       \expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@
       \else
@@ -5926,6 +6245,7 @@
                               &\csname shade@style\the\loopcount\endcsname)}
          \fi
       \ifnum\loopcount<\seq@count \repeat
+      \fi
 }
 
 \def\getregion@fromemphstack@first{%
@@ -6084,7 +6404,6 @@
 }
 
 \def\calc@frame{%
-      \advance\pos@count by -1
       \loopcount=-1 \innerloopcount=0
       \loop
          \advance\loopcount by 1
@@ -6144,7 +6463,6 @@
             \fi
          \fi\fi
       \ifnum\loopcount<\seq@count \repeat
-      \advance\pos@count by 1
 }
 
 \def\get@nextres#1#2:{%
@@ -6871,7 +7189,6 @@
 }
 
 \def\calc@feature{%
-      \advance\pos@count by -1
       \loopcount=-1 \innerloopcount=0
       \loop
          \advance\loopcount by 1
@@ -7176,12 +7493,31 @@
          \fi
          \fi
       \ifnum\loopcount<\seq@count \repeat
-      \advance\pos@count by 1
 }
 
 \def\c@nsensus{%
  \ifnum\pos@count>\res@perline
     \else
+    \global\advance\cons@count by 1\relax
+    \ifnum\cons@count=0\relax
+       \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi
+    \fi
+    \expandafter\xdef\csname res@count0\endcsname{\the\cons@count}
+    \ifx\hide@true\y@
+    \expandafter\ifx\csname hidestart0\endcsname\ampers@nd
+    \else
+       \expandafter\ifnum\csname hidestart0\endcsname>\cons@count
+       \else
+          \expandafter\ifnum\csname hidestop0\endcsname<\cons@count
+          \else
+             \xdef\hide@now{y} \xdef\eighth@{0}
+          \fi
+          \expandafter\ifnum\csname hidestop0\endcsname=\cons@count
+             \getregion@fromhidestack{0}
+          \fi
+    \fi
+    \fi
+    \fi
     \loopcount=0
     \loop
          \advance\loopcount by 1
@@ -7199,74 +7535,112 @@
                 \ifx\allow@zero\n@ \advance\res@count by 1 \fi
              \fi
              \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
+             \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
+             \ifx\hide@true\y@
+             \expandafter\ifx\csname hidestart\the\loopcount\endcsname\ampers@nd
+             \else
+             \expandafter\ifnum\csname hidestart\the\loopcount\endcsname>\res@count
+             \else
+                \expandafter\ifnum\csname hidestop\the\loopcount\endcsname<\res@count
+                \else
+                   \xdef\hide@now{y}\xdef\eighth@{\the\loopcount}
+                \fi
+                \expandafter\ifnum\csname hidestop\the\loopcount\endcsname=\res@count
+                   \xdef\first@@{\first@}
+                   \expandafter\getregion@fromhidestack{\the\loopcount}
+                   \xdef\first@{\first@@}
+                \fi
+             \fi
+             \fi
+             \fi
              \ifnum\loopcount=\rule@num\relax
               \expandafter\ifnum\csname res@count\rule@num\endcsname=\rule@tens
-                \xdef\ruler@{\ruler@ !<\rule@tens>}
+                \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
+                   \xdef\temp@{\rule@tens}
+                \else
+                   \xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
+                \fi
+                \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi
                 \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
                 \ifnum\innerloopcount=0
                    \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
                 \fi
                 \xdef\rule@tens{\the\innerloopcount}
               \else
-                \xdef\ruler@{\ruler@ -}
+                \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi
+              \fi
+              \xdef\temp@{\csname res@count\rule@num\endcsname}
+              \expandafter\ifx\csname alt@ruler\temp@\endcsname\relax
+              \else
+                \expandafter\xdef\csname alt@ruler\temp@\endcsname{\temp@}
               \fi
              \fi
-          \ifx\collect@valtop\yes
-          \ifnum\v@lseqtop=\loopcount
-             \xdef\v@ltop{\v@ltop,\csname \ffourth@top\first@\endcsname}
-          \fi\fi
-          \ifx\collect@valttop\yes
-          \ifnum\v@lseqttop=\loopcount
-             \xdef\v@lttop{\v@lttop,\csname \ffourth@ttop\first@\endcsname}
-          \fi\fi
-          \ifx\collect@valbottom\yes
-          \ifnum\v@lseqbottom=\loopcount
-             \xdef\v@lbottom{\v@lbottom,\csname \ffourth@bottom\first@\endcsname}
-          \fi\fi
-          \ifx\collect@valbbottom\yes
-          \ifnum\v@lseqbbottom=\loopcount
-             \xdef\v@lbbottom{\v@lbbottom,\csname \ffourth@bbottom\first@\endcsname}
-          \fi\fi
-          \ifx\collect@restop\yes
-          \ifnum\tr@nsseqtop=\loopcount
-             \xdef\last@restop{\last@@restop}
-             \xdef\tr@nslatetop{\tr@nslatetop\first@}
-             \xdef\last@@restop{\first@}
-             \innerloopcount=\triple@counttop
-             \advance\innerloopcount by 1
-             \ifnum\innerloopcount>3 \innerloopcount=1 \fi
-             \xdef\triple@counttop{\the\innerloopcount}
-          \fi\fi
-          \ifx\collect@resttop\yes
-          \ifnum\tr@nsseqttop=\loopcount
-             \xdef\last@resttop{\last@@resttop}
-             \xdef\tr@nslatettop{\tr@nslatettop\first@}
-             \xdef\last@@resttop{\first@}
-             \innerloopcount=\triple@countttop
-             \advance\innerloopcount by 1
-             \ifnum\innerloopcount>3 \innerloopcount=1 \fi
-             \xdef\triple@countttop{\the\innerloopcount}
-          \fi\fi
-          \ifx\collect@resbottom\yes
-          \ifnum\tr@nsseqbottom=\loopcount
-              \xdef\last@resbottom{\last@@resbottom}
-              \xdef\tr@nslatebottom{\tr@nslatebottom\first@}
-              \xdef\last@@resbottom{\first@}
-              \innerloopcount=\triple@countbottom
-              \advance\innerloopcount by 1
-              \ifnum\innerloopcount>3 \innerloopcount=1 \fi
-              \xdef\triple@countbottom{\the\innerloopcount}
-          \fi\fi
-          \ifx\collect@resbbottom\yes
-          \ifnum\tr@nsseqbbottom=\loopcount
-              \xdef\last@resbbottom{\last@@resbbottom}
-              \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@}
-              \xdef\last@@resbbottom{\first@}
-              \innerloopcount=\triple@countbbottom
-              \advance\innerloopcount by 1
-              \ifnum\innerloopcount>3 \innerloopcount=1 \fi
-              \xdef\triple@countbbottom{\the\innerloopcount}
-          \fi\fi
+             \ifx\hide@now\n@
+             \ifx\collect@valtop\yes
+             \ifnum\v@lseqtop=\loopcount
+                \xdef\v@ltop{\v@ltop,\csname \ffourth@top\first@\endcsname}
+             \fi\fi
+             \ifx\collect@valttop\yes
+             \ifnum\v@lseqttop=\loopcount
+                \xdef\v@lttop{\v@lttop,\csname \ffourth@ttop\first@\endcsname}
+             \fi\fi
+             \ifx\collect@valbottom\yes
+             \ifnum\v@lseqbottom=\loopcount
+                \xdef\v@lbottom{\v@lbottom,\csname \ffourth@bottom\first@\endcsname}
+             \fi\fi
+             \ifx\collect@valbbottom\yes
+             \ifnum\v@lseqbbottom=\loopcount
+                \xdef\v@lbbottom{\v@lbbottom,\csname \ffourth@bbottom\first@\endcsname}
+             \fi\fi
+             \fi
+             \ifx\collect@restop\yes
+             \ifnum\tr@nsseqtop=\loopcount
+                \xdef\last@restop{\last@@restop}
+                \xdef\last@@restop{\first@}
+                \ifx\hide@now\n@
+                   \xdef\tr@nslatetop{\tr@nslatetop\first@}
+                \fi
+                \innerloopcount=\triple@counttop
+                \advance\innerloopcount by 1
+                \ifnum\innerloopcount>3 \innerloopcount=1 \fi
+                \xdef\triple@counttop{\the\innerloopcount}
+             \fi\fi
+             \ifx\collect@resttop\yes
+             \ifnum\tr@nsseqttop=\loopcount
+                \xdef\last@resttop{\last@@resttop}
+                \xdef\last@@resttop{\first@}
+                \ifx\hide@now\n@
+                   \xdef\tr@nslatettop{\tr@nslatettop\first@}
+                \fi
+                \innerloopcount=\triple@countttop
+                \advance\innerloopcount by 1
+                \ifnum\innerloopcount>3 \innerloopcount=1 \fi
+                \xdef\triple@countttop{\the\innerloopcount}
+             \fi\fi
+             \ifx\collect@resbottom\yes
+             \ifnum\tr@nsseqbottom=\loopcount
+                 \xdef\last@resbottom{\last@@resbottom}
+                 \xdef\last@@resbottom{\first@}
+                 \ifx\hide@now\n@
+                    \xdef\tr@nslatebottom{\tr@nslatebottom\first@}
+                 \fi
+                 \innerloopcount=\triple@countbottom
+                 \advance\innerloopcount by 1
+                 \ifnum\innerloopcount>3 \innerloopcount=1 \fi
+                 \xdef\triple@countbottom{\the\innerloopcount}
+             \fi\fi
+             \ifx\collect@resbbottom\yes
+             \ifnum\tr@nsseqbbottom=\loopcount
+                 \xdef\last@resbbottom{\last@@resbbottom}
+                 \xdef\last@@resbbottom{\first@}
+                 \ifx\hide@now\n@
+                    \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@}
+                 \fi
+                 \innerloopcount=\triple@countbbottom
+                 \advance\innerloopcount by 1
+                 \ifnum\innerloopcount>3 \innerloopcount=1 \fi
+                 \xdef\triple@countbbottom{\the\innerloopcount}
+             \fi\fi
           \innerloopcount=\csname mol@weight\the\loopcount\endcsname
           \advance\innerloopcount by \csname \prefix@ mw\first@\endcsname
           \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{%
@@ -7276,7 +7650,8 @@
           \expandafter\xdef\csname ch@rge\the\loopcount\endcsname{%
                            \the\innerloopcount}
          \else
-          \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi
+          \ifnum\loopcount=\rule@num \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi\fi
+          \ifx\hide@now\n@
           \ifx\collect@valtop\yes
           \ifnum\v@lseqtop=\loopcount
              \xdef\v@ltop{\v@ltop,N}
@@ -7309,8 +7684,31 @@
           \ifnum\tr@nsseqbbottom=\loopcount
               \xdef\tr@nslatebbottom{\tr@nslatebbottom -}
           \fi\fi
+          \fi
          \fi
     \ifnum\loopcount<\seq@count \repeat
+       \ifnum\rule@num=0
+           \ifnum\cons@count=\rule@tens
+              \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
+                 \xdef\temp@{\rule@tens}
+              \else
+                 \xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
+              \fi
+              \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi
+              \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
+              \ifnum\innerloopcount=0
+                 \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
+              \fi
+              \xdef\rule@tens{\the\innerloopcount}
+           \else
+              \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi
+           \fi
+           \expandafter\ifx\csname alt@ruler\the\cons@count\endcsname\relax
+           \else
+             \expandafter\xdef\csname alt@ruler\the\cons@count\endcsname{\the\cons@count}
+           \fi
+       \fi
+       \ifx\hide@now\n@
          \ifx\collect@cons@graphtop\yes
                 \outerloopcount=1\relax
                 \temp@count=0\relax
@@ -7346,34 +7744,48 @@
                 \ifnum\outerloopcount<5\relax\outerloopcount=5\fi
                 \xdef\c@nscol{\c@nscol\the\outerloopcount,}
          \fi
+         \ifx\exp@rt\y@
+             \ifx\seventh@\y@
+                \outerloopcount=1\relax
+                \temp@count=0\relax
+                \sum@up@cons
+                \outerloopcount=\cons@val
+                \advance\outerloopcount by 4
+                \divide\outerloopcount by 5
+                \multiply\outerloopcount by 5
+                \ifnum\outerloopcount<5\relax\outerloopcount=5\fi
+                \xdef\seventh@{n}
+                \immediate\write\exp@rtfile{\string color col\the\outerloopcount, resi \sixth@}
+             \fi
+         \fi
+       \fi
 
-    \global\advance\cons@count by 1\relax
-    \ifnum\cons@count=0\relax
-       \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi
-    \fi
-    \expandafter\xdef\csname res@count0\endcsname{\the\cons@count}
-    \ifnum\rule@num=0
-        \ifnum\cons@count=\rule@tens
-           \xdef\ruler@{\ruler@ !<\rule@tens>}
-           \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
-           \ifnum\innerloopcount=0
-              \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
-           \fi
-           \xdef\rule@tens{\the\innerloopcount}
-        \else
-           \xdef\ruler@{\ruler@ -}
-        \fi
+%%%%%%%%%%%%%
+    \ifx\hide@now\y@
+       \regionalshadenowtrue \regionaltintnowtrue
+       \regionalemphnowtrue  \framenowtrue
     \fi
+    \ifregionalshadenow \calc@regshade \fi
+    \ifregionaltintnow  \calc@regtint  \fi
+    \ifregionalemphnow  \calc@regemph  \fi
+    \ifframenow         \calc@frame    \fi
+    \iftopfeaturenow     \xdef\bottop@{top}     \calc@feature \fi
+    \ifttopfeaturenow    \xdef\bottop@{ttop}    \calc@feature \fi
+    \ifbottomfeaturenow  \xdef\bottop@{bottom}  \calc@feature \fi
+    \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi
+    \ifx\hide@now\y@
+      \xdef\hidebar@on{1}
+      \ifnum\pos@count=\bar@pos
+      \else
+       \loopcount=\pos@count
+       \advance\loopcount by -\bar@pos
+       \xdef\bar@pos{\the\pos@count}
+       \xdef\stylehidebar{\stylehidebar\the\loopcount;\csname hidestyle\eighth@\endcsname;\csname hidetext\eighth@\endcsname;}
+      \fi
+    \else
+%%%%%%%%%%%%%
     \advance\pos@count by 1
-     \ifshow@logo        \calc@logo     \fi
-     \ifregionalshadenow \calc@regshade \fi
-     \ifregionaltintnow  \calc@regtint  \fi
-     \ifregionalemphnow  \calc@regemph  \fi
-     \ifframenow         \calc@frame    \fi
-     \iftopfeaturenow     \xdef\bottop@{top}     \calc@feature \fi
-     \ifttopfeaturenow    \xdef\bottop@{ttop}    \calc@feature \fi
-     \ifbottomfeaturenow  \xdef\bottop@{bottom}  \calc@feature \fi
-     \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi
+     \ifshow@logo         \calc@logo     \fi
      \ifall@fshade \all@funcshade
      \else
       \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi
@@ -7384,6 +7796,10 @@
       \else \xdef\c@se{1} \check@ident \fi
       \ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi
      \fi
+%%%%%%%%
+    \fi
+    \xdef\hide@now{n}
+%%%%%%%%
     \expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax
       \c@nsensus
     \else
@@ -7398,6 +7814,14 @@
     \fi
  \fi}
 
+\def\prep@reexp@rtfile{
+   \loopcount=0
+   \loop
+      \advance\loopcount by 5
+      \immediate\write\exp@rtfile{\string set_color col\the\loopcount, \csname\c@nsc@l\the\loopcount\endcsname}
+   \ifnum\loopcount>95\else\repeat
+}
+
 \def\c@unt{%
        \advance\loopcount by 1
        \xdef\seq@line{\csname sequence\the\loopcount\endcsname}
@@ -7435,8 +7859,10 @@
                      \csname sequence\the\loopcount\endcsname @}
  \ifnum\loopcount<\seq@count \repeat
  \end@count=0 \count@first \end@count=0 \xdef\start@number{0}
- \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse
- \framenowfalse
+ \ifx\hide@now\n@
+    \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse
+    \framenowfalse
+ \fi
  \topfeaturenowfalse  \bottomfeaturenowfalse
  \ttopfeaturenowfalse \bbottomfeaturenowfalse
  \innerloopcount=\cons@count
@@ -7448,7 +7874,7 @@
             \expandafter\ifnum\csname start\the\loopcount\endcsname>%
             \innerloopcount
             \else
-               \regionalshadenowtrue
+                  \regionalshadenowtrue
             \fi
          \fi
     \fi
@@ -7458,7 +7884,7 @@
             \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>%
             \innerloopcount
             \else
-               \regionaltintnowtrue
+                  \regionaltintnowtrue
             \fi
          \fi
     \fi
@@ -7468,7 +7894,8 @@
             \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>%
             \innerloopcount
             \else
-               \regionalemphnowtrue
+            \else
+                  \regionalemphnowtrue
             \fi
          \fi
     \fi
@@ -7584,7 +8011,7 @@
             \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>%
             \innerloopcount
             \else
-               \regionaltintnowtrue
+                  \regionaltintnowtrue
             \fi
          \fi
     \fi
@@ -7970,66 +8397,69 @@
 
 \def\get@rulenum<#1>#2@{%
    \xdef\first@{#2@}%
+   \xdef\fill@char{#1[,]&}%
+   \expandafter\opt@color\fill@char%
+   \ifx\f@color\comm@\xdef\f@color{\ruler@fg}\fi%
    \ifcase\rule@top
      \ifnum\ruler@rot=0 %
       \xdef\temp@{tt}%
       \ifx\ruler@family\temp@%
-         \def\third@{\ensuremath{\,\stackrel{\mathtt{#1}}{.}}}%
+         \def\third@{\ensuremath{\,\stackrel{\mathtt{\fourth@}}{\textcolor{\ruler@fg}{.}}}}%
       \else
       \xdef\temp@{sf}%
       \ifx\ruler@family\temp@%
-         \def\third@{\ensuremath{\,\stackrel{\mathsf{#1}}{.}}}%
+         \def\third@{\ensuremath{\,\stackrel{\mathsf{\fourth@}}{\textcolor{\ruler@fg}{.}}}}%
       \else
       \xdef\temp@{rm}%
       \ifx\ruler@family\temp@%
-         \def\third@{\ensuremath{\,\stackrel{\mathrm{#1}}{.}}}%
+         \def\third@{\ensuremath{\,\stackrel{\mathrm{\fourth@}}{\textcolor{\ruler@fg}{.}}}}%
       \fi\fi\fi
      \else
       \xdef\temp@{tt}%
       \ifx\ruler@family\temp@%
          \def\third@{\tt\bottomruler@size\,\,\,\,%
-           \begin{rotopo}{90}\hbox to \ruler@width{\,\ensuremath{\cdot}\,#1\hss}\end{rotopo}}%
+           \begin{rotopo}{90}\hbox to \ruler@width{\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}\,\fourth@\hss}\end{rotopo}}%
       \else
       \xdef\temp@{sf}%
       \ifx\ruler@family\temp@%
          \def\third@{\sf\bottomruler@size\,\,\,\,%
-           \begin{rotopo}{90}\hbox to \ruler@width{\,\ensuremath{\cdot}\,#1\hss}\end{rotopo}}%
+           \begin{rotopo}{90}\hbox to \ruler@width{\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}\,\fourth@\hss}\end{rotopo}}%
       \else
       \xdef\temp@{rm}%
       \ifx\ruler@family\temp@%
          \def\third@{\rm\bottomruler@size\,\,\,\,%
-           \begin{rotopo}{90}\hbox to \ruler@width{\,\ensuremath{\cdot}\,#1\hss}\end{rotopo}}%
+           \begin{rotopo}{90}\hbox to \ruler@width{\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}\,\fourth@\hss}\end{rotopo}}%
       \fi\fi\fi
      \fi
    \else
      \ifnum\ruler@rot=0 %
       \xdef\temp@{tt}%
       \ifx\ruler@family\temp@%
-         \def\third@{\bottomruler@size\ensuremath{\,\stackrel{.}{\mathtt{#1}}}}%
+         \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\textcolor{\ruler@fg}{.}}{\mathtt{\fourth@}}}}%
       \else
       \xdef\temp@{sf}%
       \ifx\ruler@family\temp@%
-         \def\third@{\bottomruler@size\ensuremath{\,\stackrel{.}{\mathsf{#1}}}}%
+         \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\textcolor{\ruler@fg}{.}}{\mathsf{\fourth@}}}}%
       \else
       \xdef\temp@{rm}%
       \ifx\ruler@family\temp@%
-         \def\third@{\bottomruler@size\ensuremath{\,\stackrel{.}{\mathrm{#1}}}}%
+         \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\textcolor{\ruler@fg}{.}}{\mathrm{\fourth@}}}}%
       \fi\fi\fi
      \else
       \xdef\temp@{tt}%
       \ifx\ruler@family\temp@%
          \def\third@{\tt\bottomruler@size\,\,\,\,%
-           \begin{rotopo}{90}\hbox to \ruler@width{\hss#1\,\ensuremath{\cdot}}\end{rotopo}}%
+           \begin{rotopo}{90}\hbox to \ruler@width{\hss\fourth@\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}}\end{rotopo}}%
       \else
       \xdef\temp@{sf}%
       \ifx\ruler@family\temp@%
          \def\third@{\sf\bottomruler@size\,\,\,\,%
-           \begin{rotopo}{90}\hbox to \ruler@width{\hss#1\,\ensuremath{\cdot}}\end{rotopo}}%
+           \begin{rotopo}{90}\hbox to \ruler@width{\hss\fourth@\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}}\end{rotopo}}%
       \else
       \xdef\temp@{rm}%
       \ifx\ruler@family\temp@%
          \def\third@{\rm\bottomruler@size\,\,\,\,%
-           \begin{rotopo}{90}\hbox to \ruler@width{\hss#1\,\ensuremath{\cdot}}\end{rotopo}}%
+           \begin{rotopo}{90}\hbox to \ruler@width{\hss\fourth@\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}}\end{rotopo}}%
       \fi\fi\fi
      \fi
    \fi}
@@ -8039,8 +8469,8 @@
    \xdef\first@{#2@}%
    \xdef\second@{!}%
    \ifx\third@\second@ \expandafter\get@rulenum\first@%
-   \else \xdef\third@{}\fi
-   \hbox to \box@width{\hss\third@\hss}%
+   \else \xdef\third@{}\xdef\f@color{Black}\fi
+   \textcolor{\f@color}{\hbox to \box@width{\hss\third@\hss}}%
    }
 
 \def\put@rulechar{%
@@ -8081,7 +8511,7 @@
    \fontseries{m}%
    \fontshape{n}%
    \selectfont%
-   \innerloopcount=1\relax\textcolor{\ruler@fg}{\put@rulechar}%
+   \innerloopcount=1\relax\put@rulechar%
    \newline\hbox{}%
 }
 \def\get@firstfill#1#2&{\xdef\second@@{#1}\xdef\fill@char{#2&}}
@@ -8743,6 +9173,124 @@
    \fi%
    \fi%
 }
+\def\next@hidebar#1;#2;#3;#4@{%
+   \xdef\first@{#1}%
+   \ifx\first@\ampers@nd%
+   \else%
+      \fontfamily{\hideblock@family}\fontseries{\hideblock@series}%
+      \fontshape{\hideblock@shape}%
+      \selectfont%
+      \newline\hbox{}%
+      \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi%
+      \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+      \hbox to -\box@width{\hss}%
+      \kern-0.1\box@width%
+      \xdef\last@{#3[,]&}\expandafter\opt@color\last@%
+      \ifx\f@color\comm@\xdef\f@color{Black}\fi%
+      \textcolor{\f@color}{%
+      \hbox to \first@\box@width{}%
+      \hbox to 0pt{\hss\strut\hideblock@size{\,\fourth@}\hss}}%
+      \xdef\last@{#2[,]&}\expandafter\opt@color\last@%
+      \ifx\f@color\comm@\xdef\f@color{Black}\fi%
+      \vspace{-0.23\box@height}%
+      \xdef\temp@{triangle}%
+      \ifx\fourth@\temp@%
+      \else
+      \xdef\temp@{square}%
+      \ifx\fourth@\temp@%
+      \else
+      \xdef\temp@{none}%
+      \ifx\fourth@\temp@%
+      \else
+      \vspace{-0.06\box@height}%
+      \fi\fi\fi%
+      \newline\hbox{}%
+      \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi%
+      \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+      \hbox to -\box@width{\hss}%
+      \hbox to \first@\box@width{}%
+      \kern-0.1\box@width%
+      \textcolor{\f@color}{%
+      \raisebox{0.47\box@height}{\rule{0.2\box@width}{\temp@@length}}%
+      \xdef\first@{triangle}%
+      \ifx\fourth@\first@%
+         \kern-0.582\box@width%
+         \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigtriangledown$\hss}}%
+         \kern-0.418\box@width%
+      \else
+         \xdef\first@{square}%
+         \ifx\fourth@\first@%
+            \kern-0.6\box@width%
+            \raisebox{-0.12\box@height}{%
+            \raisebox{\temp@@length}{\hbox to \box@width{\hss$\square$\hss}}}%
+            \raisebox{-0.19\box@height}{%
+            \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}%
+            \kern-1.4\box@width%
+         \else
+            \xdef\first@{none}%
+            \ifx\fourth@\first@%
+               \kern-0.6\box@width%
+               \raisebox{-0.19\box@height}{%
+               \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}%
+               \kern-0.4\box@width%
+            \else
+               \kern-0.6\box@width%
+               \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigodot$\hss}}%
+               \kern-0.4\box@width%
+            \fi%
+         \fi%
+      \fi%
+      \kern-0.58\box@width%
+      \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bullet$\hss}}%
+      \xdef\first@{#4@}}%
+   \fi
+}
+\def\put@@hidebar{%
+   \if\first@ @%
+   \else
+      \hbox to -\box@width{\hss}%
+      \expandafter\next@hidebar\first@%
+      \put@@hidebar%
+   \fi%
+}
+\def\put@hidebar{%
+   \ifx\hide@seqs\n@%
+   \ifshow@cons\ifnum\cons@top=1 \vspace{-\baselineskip}\fi\fi%
+   \temp@count=\seq@count%
+   \advance\temp@count by 1%
+   \ifx\hide@seqs\y@
+      \advance\temp@count by -1 %
+   \else%
+   \loopcount=1%
+   \xdef\first@{true}%
+   \loop%
+      \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@%
+         \advance\temp@count by -1\fi%
+      \advance\loopcount by 1%
+   \ifnum\loopcount>\seq@count\else\repeat%
+   \fi
+   \ifnum\temp@count>0%
+   \setlength\temp@@length{\box@height}%
+   \advance\temp@@length by \box@depth%
+   \setlength\arrow@height{0.5\temp@@length}%
+   \setlength\temp@@length{\temp@count\temp@@length}%
+   \advance\temp@@length by \arrow@height%
+   \advance\temp@@length by -0.75\box@height%%%%%%%
+   \setlength\arrow@width{\sep@space}%
+   \setlength\arrow@width{\seq@gap@num\arrow@width}%
+   \advance\temp@@length by \arrow@width%
+   \vspace{\arrow@height}%
+   \vspace{-\temp@@length}%
+   \vspace{-2.56\baselineskip}%
+   \xdef\first@{\stylehidebar @}%
+   \put@@hidebar%
+   \vspace{-\arrow@height}%
+   \vspace{-0.47\box@height}%
+   \ifshow@cons\ifnum\cons@top=1 \vspace{\baselineskip}\fi\fi%
+   \newline\hbox{}%
+   \fi%
+   \fi%
+}
 \def\decimal@A#1#2@{%
    \def\decimal@AB##1##2@{\xdef\temp@{##1.##2}}%
    \xdef\temp@@{#1}%
@@ -9180,7 +9728,7 @@
 
 \def\set@lines{%
    \pos@count=1
-   \xdef\frame@pos{1}%
+   \xdef\frame@pos{1}\xdef\bar@pos{0}\xdef\hidebar@on{0}%
    \xdef\featurepostop{1}\xdef\featureposbottom{1}%
    \xdef\featureposttop{1}\xdef\featureposbbottom{1}%
    \findc@nsensus%
@@ -9280,6 +9828,9 @@
       \ifnum\frame@on=0 \xdef\frame@{0}\fi%
       \put@frame%
    \fi%
+   \ifnum\hidebar@on=1 %
+      \put@hidebar%
+   \fi%
    \ifshow@logo\ifnum\logo@top=1 %
       \xdef\last@{\stack@sequencelogo @}%
       \ifx\logo@name@user\ampers@nd\xdef\logo@name{logo}\else\xdef\logo@name{\logo@name@user}\fi
@@ -9345,7 +9896,7 @@
       \fi
    \fi
    \xdef\consensus{} \xdef\ruler@{}
-   \xdef\styleframe{}
+   \xdef\styleframe{}       \xdef\stylehidebar{}
    \xdef\textfeaturetop{}   \xdef\textfeaturebottom{}
    \xdef\textfeaturettop{}  \xdef\textfeaturebbottom{}
    \xdef\stylefeaturetop{}  \xdef\stylefeaturebottom{}
@@ -9457,7 +10008,7 @@
     \xdef\textfeaturettop{}   \xdef\featureonttop{0}
     \xdef\textfeaturebottom{} \xdef\featureonbottom{0}
     \xdef\textfeaturebbottom{}\xdef\featureonbbottom{0}
-    \xdef\styleframe{}
+    \xdef\styleframe{}        \xdef\stylehidebar{}
     \xdef\stylefeaturetop{}
     \xdef\stylefeaturettop{}
     \xdef\stylefeaturebottom{}
@@ -9550,6 +10101,7 @@
        \res@count=0
        \innerloopcount=0
        \residue@count
+       \if\seq@type A \guess@DNA \fi
        \advance\seq@pointer by \res@count\relax
        \xdef\total@pos{\the\total@count}
        \ifnum\end@num>\end@count\relax\xdef\end@num{\the\end@count}\fi
@@ -9593,6 +10145,7 @@
        \res@count=0
        \innerloopcount=0
        \residue@count
+       \if\seq@type A \guess@DNA \fi
        \advance\seq@pointer by \res@count
        \xdef\total@pos{\the\total@count}
        \ifnum\end@num>\end@count\relax\xdef\end@num{\the\end@count}\fi
@@ -9614,6 +10167,7 @@
     \else \start@true \fi
     \res@count=0 \seq@pointer=0 \end@count=0 \total@count=0
     \xdef\start@number{0}
+    \ifx\exp@rt\y@ \prep@reexp@rtfile \fi
     \ifx\f@st@\y@
        \loopcount=0
        \read@fasta
@@ -9621,7 +10175,6 @@
        \loopcount=1
        \read@loop
     \fi
-    \if\seq@type A \guess@DNA \fi
     \ifnum\seq@pointer>0
        \ifstop@
        \else
@@ -9631,6 +10184,7 @@
        \fi
     \fi
     \ifshow@sublogo \closein\sublogofile \fi
+    \ifx\exp@rt\y@ \closeout\exp@rtfile \fi
     \closein\alignfile
     \message{)}
 }
@@ -9729,6 +10283,7 @@
     \loopcount=0 \xdef\seq@order{}
     \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
     \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
+    \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@}
     \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@}
     \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@}
     \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
@@ -9752,6 +10307,7 @@
        \expandafter\xdef\csname number@col\the\loopcount\endcsname{yes}
        \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
        \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
+       \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@}
        \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@}
        \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@}
        \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
@@ -9795,6 +10351,7 @@
    \ifshow@cons\setbox1=\hbox{\cons@name}\name@width=\wd1\else\name@width=0pt\fi
    \loopcount=0
    \expandafter\getregion@fromstack{\the\loopcount}
+   \expandafter\getregion@fromhidestack{\the\loopcount}
    \expandafter\getregion@fromtintstack{\the\loopcount}
    \expandafter\getregion@fromemphstack{\the\loopcount}
    \expandafter\getregion@fromframestack{\the\loopcount}
@@ -9841,6 +10398,7 @@
           \baselineskip=\box@height \advance\baselineskip by \box@depth
        \fi
        \expandafter\getregion@fromstack{\the\loopcount}
+       \expandafter\getregion@fromhidestack{\the\loopcount}
        \expandafter\getregion@fromtintstack{\the\loopcount}
        \expandafter\getregion@fromemphstack{\the\loopcount}
        \expandafter\getregion@fromframestack{\the\loopcount}
@@ -10149,6 +10707,10 @@
 \xdef\logo@name@user{&}   \xdef\sublogo@name@user{&}
 \expandafter\xdef\csname group@num1\endcsname{0}
 \expandafter\xdef\csname group@num2\endcsname{0}
+\xdef\exp@rt@num{0}       \xdef\exp@rt{n}
+\xdef\hide@true{n}        \xdef\hide@now{n}
+\xdef\hide@label{circ}
+\xdef\divref@{0}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%                                                                      %%%%%
@@ -10232,6 +10794,10 @@
 \setseries{featurestyles}{md}       %  Use normal series for feature styles
 \setshape {featurestyles}{up}       %  Use upright shape for feature styles
 \setsize {featurestyles}{normalsize}%  Use normal size for feature styles
+\setfamily{hideblock}{rm}           %  Use roman family for hidden block labels
+\setseries{hideblock}{md}           %  Use normal series for hidden block labels
+\setshape {hideblock}{it}           %  Use italics shape for hidden block labels
+\setsize  {hideblock}{normalsize}   %  Use normal size for hidden block labels
 \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