diff --git a/doc/README.results b/doc/README.results
new file mode 100644
index 0000000..341b2be
--- /dev/null
+++ b/doc/README.results
@@ -0,0 +1,29 @@
+Name1:		Protein 1 name
+msa1:		Protein 1 UniProt ID
+Name2:		Protein 2 name
+msa2:		Protein 2 Uniprot ID
+colA:		Position of residue "A" from Protein 1 in the MSA
+realA:		Position of residue "A" from Protein 1 in the non-aligned sequence of the reference organism
+colB:		Position of residue "B" from Protein 2 in the MSA
+realB:		Position of residue "B" from Protein 3 in the non-aligned sequence of the reference organism
+seq1:		Position and amino-acid of residue "A" from Protein 1 in the non-aligned, non-filtered by gblocks sequence of the reference organism
+seq2:		Position and amino-acid of residue "A" from Protein 1 in the non-aligned, non-filtered by gblocks sequence of the reference organism
+meanA:		meanA
+meanB:		meanB
+corr:		Co-evolutionary correlation (non corrected)
+boot:		Bootstrap value of the correlation
+corrT:		Correlation threshold for each pair of proteins
+cCoev:		Co-evolutionary correlation (corrected, normalized to threshold)
+pvalA:		Correlation p-value for A->B (non-corrected)
+pvalB:		Correlation p-value for B->A (non-corrected)
+pMean:		Mean correlation p-value (non-corrected)
+pDiff:		Difference between pvalA-pvalB (absolute value)
+corr1:		Correlation for A->B (non-corrected)
+corr2:		Correlation for B->A (non-corrected)
+bonferroni:	Bonferroni corrected pMean
+GapA:		MSA column gaps (-) for residue "A"
+GapB:		MSA column gaps (-) for residue "B"
+GapAB:		Mean value of GapA and GapB
+DivA:		Diversity within MSA column for residue "A"
+DivB:		Diversity within MSA column for residue "B"
+DivAB:		Mean value of DivA and DivB
diff --git a/end.sh b/end.sh
new file mode 100644
index 0000000..d4d4a45
--- /dev/null
+++ b/end.sh
@@ -0,0 +1,149 @@
+#!/bin/bash
+
+# Export all
+set -a
+
+# What date and time is it?
+DATESTAMP=$(date)
+
+# Current work dir
+CWD=$(pwd)
+
+# Load settings first
+. $CWD/settings.conf
+
+# Load functions
+. $CWD/functions/databases.sh
+. $CWD/functions/retrieval.sh
+. $CWD/functions/blast.sh
+. $CWD/functions/msa.sh
+. $CWD/functions/trees.sh
+. $CWD/functions/pairing.sh
+. $CWD/functions/caps.sh
+. $CWD/functions/results.sh
+. $CWD/functions/network.sh
+. $CWD/functions/check.sh
+
+EGAPS="0.8" # Gaps score cut
+EPDIF="0.0011"
+
+ETSV="$TMP/$RESULTS/pairs-P${PVALUE}-B${BONFERRONI}.tsv"
+EOUT="filtered-P${PVALUE}-pDiff${EPDIF}-Bonf${BONFERRONI}.tsv"
+ENET="FILTERED-P${PVALUE}-pDiff${EPDIF}-Bonf${BONFERRONI}.xml"
+
+# Let user change work dir here as well
+read -p "Change working dir or press ENTER to accept: " -e -i $TMP TMP
+mkdir -p $TMP
+
+# Specify the input file
+echo -e "\n\e[96mEnter the full path to the pairs-P${PVALUE}-B${BONFERRONI}.tsv file:\e[39m"
+read -e -i $ETSV ETSV
+
+rm -rf $TMP/$RESULTS/pairs-P${PVALUE}-B${BONFERRONI}
+mkdir -p $TMP/$RESULTS/pairs-P${PVALUE}-B${BONFERRONI}
+
+sed 1d "$ETSV" | while read -r Name1 msa1 Name2 msa2 colA realA colB realB seq1 seq2 flt1 flt2 meanA meanB corr boot corrT cCoev pvalA pvalB pMean pDiff corr1 corr2 bonferroni GapA GapB GapAB DivA DivB DivAB ; do
+  if [ "$flt1" = "#" ] && [ "$flt2" = "#" ]; then
+    echo "Pair from a good quality MSA"
+    if (( $(echo "$GapA > $EGAPS" |bc -l) && $(echo "$GapB > $EGAPS" |bc -l) && $(echo "$pDiff < $EPDIF" |bc -l) )); then
+      echo "$Name1 $msa1 $Name2 $msa2 $cCoev $pvalA $pvalB $pMean $bonferroni $boot" >> $TMP/$RESULTS/pairs-P${PVALUE}-B${BONFERRONI}/$msa1-$msa2.tsv
+      echo "Consider $Name1 $msa1 <-> $Name2 $msa2"
+    else
+      echo "Skipping $Name1 $msa1 <-> $Name2 $msa2"
+    fi
+  else
+    echo "pair from a bad quality MSA"
+  fi
+done
+
+cd $TMP/$RESULTS/pairs-P${PVALUE}-B${BONFERRONI}
+  for pair in * ; do
+        namesIDs=$(head -n 1 $pair | awk '{print $1,$2,$3,$4}')
+      coevNumber=$(awk '{print $5}' $pair | datamash count 1)
+      
+        cCoevMAX=$(awk '{print $5}' $pair | datamash max 1)
+       cCoevMEAN=$(awk '{print $5}' $pair | datamash mean 1)
+        cCoevMIN=$(awk '{print $5}' $pair | datamash min 1)
+       cCoevSDEV=$(awk '{print $5}' $pair | datamash sstdev 1)
+       
+         bootMAX=$(awk '{print $10}' $pair | datamash max 1)
+        bootMEAN=$(awk '{print $10}' $pair | datamash mean 1)
+         bootMIN=$(awk '{print $10}' $pair | datamash min 1)
+	bootSDEV=$(awk '{print $10}' $pair | datamash sstdev 1)
+       
+        pMeanMIN=$(awk '{print $8}' $pair | datamash min 1)
+       pMeanMEAN=$(awk '{print $8}' $pair | datamash mean 1)
+        pMeanMAX=$(awk '{print $8}' $pair | datamash max 1)
+       pMeanSDEV=$(awk '{print $8}' $pair | datamash sstdev 1)
+       
+   BonferroniMIN=$(awk '{print $9}' $pair | datamash min 1)
+  BonferroniMEAN=$(awk '{print $9}' $pair | datamash mean 1)
+   BonferroniMAX=$(awk '{print $8}' $pair | datamash max 1)
+  BonferroniSDEV=$(awk '{print $8}' $pair | datamash sstdev 1)
+
+  echo "$namesIDs $coevNumber $cCoevMIN $cCoevMAX $cCoevMEAN $cCoevSDEV $bootMIN $bootMEAN $bootMAX $bootSDEV $pMeanMIN $pMeanMAX $pMeanMEAN $pMeanSDEV $BonferroniMIN $BonferroniMAX $BonferroniMEAN $BonferroniSDEV" >> $TMP/$RESULTS/$EOUT
+  echo "Processed $pair"
+done
+
+sed -i "1i Name1 msa1 Name2 msa2 coevNumber cCoevMIN cCoevMAX cCoevMEAN cCoevSDEV bootMIN bootMEAN bootMAX bootSDEV pMeanMIN pMeanMAX pMeanMEAN pMeanSDEV BonferroniMIN BonferroniMAX BonferroniMEAN BonferroniSDEV" $TMP/$RESULTS/$EOUT
+
+# Prepare the XML header
+cat << EOF >> $TMP/$RESULTS/$ENET
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<graph label="AutoCoEv" directed="0" cy:documentVersion="3.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:cy="http://www.cytoscape.org" xmlns="http://www.cs.rpi.edu/XGMML">
+  <att name="networkData">
+    <rdf:RDF>
+      <rdf:Description rdf:about="http://www.cytoscape.org/">
+        <dc:type>Protein-Protein Interaction</dc:type>
+        <dc:description>N/A</dc:description>
+        <dc:identifier>N/A</dc:identifier>
+        <dc:date>$DATE</dc:date>
+        <dc:title>CAPS</dc:title>
+        <dc:source>http://www.cytoscape.org/</dc:source>
+        <dc:format>Cytoscape-XGMML</dc:format>
+      </rdf:Description>
+    </rdf:RDF>
+  </att>
+  <att name="name" value="${MSAMETHOD}; ${GBLOCKS}; ${TREESCAPS}; ${PHYMLGUIDE}; ${TREESROOT}" type="string" cy:type="String"/>
+  <att name="MSA method" value="${MSAMETHOD}" type="string" cy:type="String"/>
+  <att name="Tree calculation" value="${TREESCAPS}" type="string" cy:type="String"/>
+  <att name="Guide tree used?" value="${PHYMLGUIDE}" type="string" cy:type="String"/>
+  <att name="Tree rooted?" value="${TREESROOT}" type="string" cy:type="String"/>
+EOF
+
+# Add nodes.
+sed 1d $TMP/tsv/proteinsFound.tsv | while read -r idxml namexml attribute; do
+echo -e "Adding node $idxml $namexml $attribute in $TMP/$RESULTS/$ENET"
+cat << EOF >> $TMP/$RESULTS/$ENET
+  <node id="$idxml" label="$namexml">
+    <att name="shared name" value="$idxml" type="string" cy:type="String"/>
+    <att name="name" value="$namexml" type="string" cy:type="String"/>
+    <att name="attribute" value="$attribute" type="string" cy:type="String"/>
+    <att name="URL" value="https://www.uniprot.org/uniprot/$idxml" type="string" cy:type="String"/>
+  </node>
+EOF
+done
+
+# Add edges
+sed 1d $TMP/$RESULTS/$EOUT | \
+while read -r Name1 msa1 Name2 msa2 coevNumber cCoevMIN cCoevMAX cCoevMEAN cCoevSDEV bootMIN bootMEAN bootMAX bootSDEV pMeanMIN pMeanMAX pMeanMEAN pMeanSDEV BonferroniMIN BonferroniMAX BonferroniMEAN BonferroniSDEV ; do
+echo -e "Adding edge: $msa1-$msa2 in $TMP/$RESULTS/$ENET"
+cat << EOF >> $TMP/$RESULTS/$ENET
+  <edge id="$Name1-$Name2" label="$Name1 - $Name2" source="$msa1" target="$msa2" cy:directed="0">
+    <att name="shared name" value="$msa1 - $msa2" type="string" cy:type="String"/>
+    <att name="shared interaction" value="Coevolution" type="string" cy:type="String"/>
+    <att name="name" value="$Name1 - $Name2" type="string" cy:type="String"/>
+    <att name="interaction" value="Coevolution" type="string" cy:type="String"/>
+    <att name="Number of coevolving sites" value="$coevNumber" type="real" cy:type="Double"/>
+    <att name="Normalized correlation (max)" value="$cCoevMAX" type="real" cy:type="Double"/>
+    <att name="Normalized correlation (mean)" value="$cCoevMEAN" type="real" cy:type="Double"/>
+    <att name="Bootstrap value (max)" value="$bootMAX" type="real" cy:type="Double"/>
+    <att name="Bootstrap value (mean)" value="$bootMEAN" type="real" cy:type="Double"/>
+    <att name="P-value non-corrected (min)" value="$pMeanMIN" type="real" cy:type="Double"/>
+    <att name="P-value non-corrected (mean)" value="$pMeanMEAN" type="real" cy:type="Double"/>
+    <att name="P-value Bonferroni (min)" value="$BonferroniMIN" type="real" cy:type="Double"/>
+    <att name="P-value Bonferroni (mean)" value="$BonferroniMEAN" type="real" cy:type="Double"/>
+  </edge>
+EOF
+done
+echo "</graph>" >> $TMP/$RESULTS/$ENET
diff --git a/examples/negatome_mouse.tsv b/examples/negatome_mouse.tsv
new file mode 100644
index 0000000..90af958
--- /dev/null
+++ b/examples/negatome_mouse.tsv
@@ -0,0 +1,406 @@
+Q64343	Abcg1
+Q7TMS5	Abcg2
+Q9DBM0	Abcg8
+P21836	Ache
+Q9QZQ1	Afdn
+A2ASQ1	Agrn
+O08915	Aip
+O08715	Akap1
+P31750	Akt1
+Q920R0	Als2
+Q8VHG2	Amot
+Q02357	Ank1
+Q3UMR0	Ankrd27
+Q6DQH2	Apbb2
+P62331	Arf6
+Q6Y5D8	Arhgap10
+Q91YM2	Arhgap35
+P53762	Arnt
+Q9WTL8	Arntl
+Q6NXK8	Asic1
+O35625	Axin1
+O08734	Bak1
+Q07813	Bax
+P21237	Bdnf
+P25916	Bmi1
+P21274	Bmp2
+O55003	Bnip3
+Q9ESU6	Brd4
+Q7TSA3	Btla
+O70355	Btnl2
+P98086	C1qa
+P28651	Ca8
+P28652	Camk2b
+Q8VHK1	Caskin2
+Q08024	Cbfb
+P30658	Cbx2
+Q6PDY0	Ccdc85b
+Q5SNZ0	Ccdc88a
+P10855	Ccl3
+P14097	Ccl4
+P30882	Ccl5
+Q9QWV9	Ccnt1
+P51680	Ccr4
+P31041	Cd28
+P27512	Cd40
+P27548	Cd40lg
+P60766	Cdc42
+P09803	Cdh1
+Q03147	Cdk7
+P46414	Cdkn1b
+P53566	Cebpa
+P28033	Cebpb
+Q00322	Cebpd
+Q03059	Chat
+O08785	Clock
+Q9JJZ9	Cngb3
+Q01147	Creb1
+P45481	Crebbp
+P27699	Crem
+P01587	Csf2
+P26955	Csf2rb
+P50462	Csrp3
+P56546	Ctbp2
+P09793	Ctla4
+Q02248	Ctnnb1
+Q9WTX6	Cul1
+P98078	Dab2
+P31786	Dbi
+Q8VHZ5	Ddit4l
+Q62108	Dlg4
+Q09163	Dlk1
+P97465	Dok1
+Q99N11	Dusp22
+P51141	Dvl1
+Q61501	E2f1
+Q8R0K9	E2f4
+Q61502	E2f5
+Q61508	Ecm1
+P57776	Eef1d
+Q8BPB5	Efemp1
+Q9WVJ9	Efemp2
+P01132	Egf
+Q01279	Egfr
+B2RWS6	Ep300
+Q8BGS1	Epb41l5
+Q03137	Epha4
+P07321	Epo
+P14753	Epor
+P25446	Fas
+P41047	Faslg
+Q08879	Fbln1
+P37889	Fbln2
+Q9WVH9	Fbln5
+P26151	Fcgr1
+Q61559	Fcgrt
+P15655	Fgf2
+P54130	Fgf9
+P16092	Fgfr1
+P21803	Fgfr2
+Q03142	Fgfr4
+O70433	Fhl2
+P35917	Flt4
+P11276	Fn1
+P70339	Frat1
+Q8C180	Frs2
+Q61584	Fxr1
+Q9WVR4	Fxr2
+Q9Z1S8	Gab2
+P17679	Gata1
+P48540	Gdnf
+P03995	Gfap
+Q9Z0G0	Gipc1
+Q9JMB0	Gkap1
+P27601	Gna13
+P08752	Gnai2
+Q6R0H7	Gnas
+P62880	Gnb2
+P63213	Gng2
+O89100	Grap2
+P23818	Gria1
+Q9WV60	Gsk3b
+Q8R4I4	Gtf2a1l
+O88895	Hdac3
+Q9Z2V6	Hdac5
+Q8C2B3	Hdac7
+Q6I6G8	Hecw2
+Q62424	Hoxa13
+P70217	Hoxd13
+O08983	Hps1
+Q99KG7	Hps4
+P38532	Hsf1
+Q05793	Hspg2
+Q9WVS0	Icos
+Q61635	Ifi47
+P05017	Igf1
+Q9QZ85	Iigp1
+P01582	Il1a
+Q61730	Il1rap
+P04351	Il2
+P01586	Il3
+P04401	Il5
+P21183	Il5ra
+P15247	Il9
+P15208	Insr
+Q8K4N8	Irak1
+P70671	Irf3
+P70434	Irf7
+P52332	Jak1
+Q62120	Jak2
+P05627	Jun
+Q02257	Jup
+P23299	Kcne1
+Q9WTW2	Kcne3
+P35918	Kdr
+Q60749	Khdrbs1
+P33175	Kif5a
+Q61768	Kif5b
+P28738	Kif5c
+P70188	Kifap3
+P05532	Kit
+O08584	Klf6
+Q6TDP3	Klhl17
+P00756	Klk1b3
+P00757	Klk1b4
+Q61097	Ksr1
+P11627	L1cam
+P63006	Lhx1
+P09056	Lif
+Q91XD2	Lims2
+Q8C129	Lnpep
+Q8BFW7	Lpp
+Q924X6	Lrp8
+P09225	Lta
+P41155	Ltb
+P20917	Mag
+Q9ESN9	Mapk8ip3
+Q6PER3	Mapre3
+Q03141	Mark3
+P28574	Max
+P97287	Mcl1
+P25206	Mcm3
+P49717	Mcm4
+Q61881	Mcm7
+P23804	Mdm2
+Q924H2	Med15
+Q80YQ2	Med23
+Q9CQA5	Med4
+Q9CZB6	Med7
+Q9D7W5	Med8
+Q60954	Meis1
+P55002	Mfap2
+Q9QZJ6	Mfap5
+A2AM29	Mllt3
+Q91V27	Mlph
+Q3UPW8	Mlxip
+Q61391	Mme
+P50538	Mxd1
+Q80US8	Mxd3
+Q60948	Mxd4
+P50540	Mxi1
+P06876	Myb
+Q7TPV4	Mybbp1a
+P01108	Myc
+P10166	Mycl
+P03966	Mycn
+Q99104	Myo5a
+Q9JK37	Myoz1
+P13595	Ncam1
+Q60974	Ncor1
+Q9WU42	Ncor2
+Q9CZA6	Nde1
+P08553	Nefm
+O35657	Neu1
+Q62414	Neurod2
+P46662	Nf2
+P01139	Ngf
+P42586	Nkx2-2
+P97503	Nkx3-2
+Q99MA9	Nkx6-1
+Q01705	Notch1
+O35516	Notch2
+Q61982	Notch3
+P31695	Notch4
+Q99J85	Nptxr
+Q62227	Nr0b2
+Q505F1	Nr2c1
+P06537	Nr3c1
+Q8CJ26	Nradd
+Q8CBD1	Nrip1
+Q9JHR9	Nrip2
+Q8R4G0	Ntng1
+Q9QXX8	Nufip1
+Q61146	Ocln
+Q9EQW6	Olig2
+Q63912	Omg
+Q61206	Pafah1b2
+Q61205	Pafah1b3
+Q8CIN4	Pak2
+P11103	Parp1
+Q2EMV9	Parp14
+Q71VB4	Pbx1
+O35984	Pbx2
+O88689	Pcdha4
+P17918	Pcna
+P63239	Pcsk1
+Q02242	Pdcd1
+P26450	Pik3r1
+Q66T02	Plekhg5
+Q8CGN5	Plin1
+Q07832	Plk1
+Q60953	Pml
+Q62009	Postn
+P35396	Ppard
+P37238	Pparg
+P63330	Ppp2ca
+Q76MZ3	Ppp2r1a
+Q99K43	Prc1
+Q5M9N9	Prdx2
+P05132	Prkaca
+P31324	Prkar2b
+P16054	Prkce
+P0C605	Prkg1
+Q61410	Prkg2
+Q9JIF0	Prmt1
+P05143	Prp2
+P15331	Prph
+P15499	Prph2
+P41593	Pth1r
+Q9QVP9	Ptk2b
+P29351	Ptpn6
+Q62132	Ptprr
+Q8K094	Pvr
+P61027	Rab10
+P62492	Rab11a
+P35292	Rab17
+P35293	Rab18
+P62821	Rab1A
+P35295	Rab20
+P35285	Rab22a
+P35288	Rab23
+Q9WTL2	Rab25
+Q9ERI2	Rab27a
+Q99KL7	Rab28
+P53994	Rab2a
+Q64008	Rab34
+Q9JKM7	Rab37
+P63011	Rab3a
+P56371	Rab4a
+Q9CQD1	Rab5a
+P35279	Rab6a
+P51150	Rab7a
+P55258	Rab8a
+Q9R0M6	Rab9a
+O35551	Rabep1
+P63001	Rac1
+Q9WTJ5	Ramp1
+Q99JI6	Rap1b
+Q922H7	Rasl11b
+P13405	Rb1
+Q60972	Rbbp4
+Q64701	Rbl1
+O08674	Rbpjl
+Q8BP92	Rcn2
+P15307	Rel
+Q04207	Rela
+Q04863	Relb
+Q60841	Reln
+P97428	Rgs16
+Q78NN4	Rgs19
+O08849	Rgs2
+P61588	Rnd3
+Q9D0C1	Rnf115
+P70336	Rock2
+P47708	Rph3a
+P18653	Rps6ka1
+Q8K0T0	Rtn1
+O70622	Rtn2
+Q9ES97	Rtn3
+Q99P72	Rtn4
+Q99PI8	Rtn4r
+Q8K0S5	Rtn4rl1
+Q7M6Z0	Rtn4rl2
+P43407	Sdc2
+O35988	Sdc4
+P63300	Selenow
+P42208	Septin2
+O55131	Septin7
+O88974	Setdb1
+P97797	Sirpa
+P53986	Slc16a1
+P13808	Slc4a2
+Q62432	Smad2
+Q8BUN5	Smad3
+P97471	Smad4
+P97454	Smad5
+O35182	Smad6
+O35253	Smad7
+O35717	Socs2
+O35718	Socs3
+Q62417	Sorbs1
+O89090	Sp1
+Q58A65	Spag9
+Q9JM90	Stap1
+P42225	Stat1
+Q00262	Stx2
+Q64704	Stx3
+P70452	Stx4
+Q8K1E0	Stx5
+O08599	Stxbp1
+Q548T0	Stxbp2
+Q60770	Stxbp3
+Q9D666	Sun1
+Q99N80	Sytl1
+Q99N50	Sytl2
+Q99N48	Sytl3
+Q549X6	Sytl4
+Q9R0Q1	Sytl4
+Q80T23	Sytl5
+Q8CF89	Tab1
+Q8R0L9	Tada3
+P70323	Tbx1
+P70371	Terf1
+Q64092	Tfe3
+P04202	Tgfb1
+Q62219	Tgfb1i1
+Q64729	Tgfbr1
+Q62312	Tgfbr2
+P21981	Tgm2
+P39447	Tjp1
+P26039	Tln1
+B9EKI3	Tmf1
+Q9D8D0	Tnfrsf13c
+P50592	Tnfsf10
+P43488	Tnfsf4
+P32972	Tnfsf8
+P41274	Tnfsf9
+Q6PFX9	Tnks
+Q3UES3	Tnks2
+O88346	Tnnt1
+P02340	Tp53
+P39429	Traf2
+P70196	Traf6
+O55055	Trdmt1
+Q9ERP3	Trim54
+Q9QUQ5	Trpc4
+Q9EP53	Tsc1
+Q61037	Tsc2
+P62500	Tsc22d1
+P25976	Ubtf
+Q8CGY6	Unc45b
+Q8K1S4	Unc5a
+Q8K1S3	Unc5b
+O08747	Unc5c
+Q00731	Vegfa
+P97946	Vegfd
+Q8BH43	Wasf2
+P22561	Wt1
+O70373	Xirp1
+P62960	Ybx1
+P62259	Ywhae
+P68254	Ywhaq
+P63101	Ywhaz
+Q80X44	Zbtb24
+Q8BN78	Zbtb33
+P17141	Zfp37
+Q62523	Zyx
diff --git a/examples/negatome_mouse_pairs.tsv b/examples/negatome_mouse_pairs.tsv
new file mode 100644
index 0000000..1a6c806
--- /dev/null
+++ b/examples/negatome_mouse_pairs.tsv
@@ -0,0 +1,1991 @@
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diff --git a/examples/raftsProteins.tsv b/examples/raftsProteins.tsv
new file mode 100644
index 0000000..9d31009
--- /dev/null
+++ b/examples/raftsProteins.tsv
@@ -0,0 +1,346 @@
+P60710	Actb	RAFT
+Q8C886	Plekhn1	RAFT
+P99024	Tubb5	RAFT
+P63017	Hspa8	RAFT
+P35700	Prdx1	RAFT
+Q62167	Ddx3x	RAFT
+P26040	Ezr	RAFT
+Q6ZWV3	Rpl10	RAFT
+P03975	Iap	RAFT
+P60843	Eif4a1	RAFT
+P58252	Eef2	RAFT
+Q9D8E6	Rpl4	RAFT
+P17182	Eno1	RAFT
+P05064	Aldoa	RAFT
+P24547	Impdh2	RAFT
+Q62351	Tfrc	RAFT
+P62830	Rpl23	RAFT
+P62754	Rps6	RAFT
+P14148	Rpl7	RAFT
+Q61656	Ddx5	RAFT
+P47911	Rpl6	RAFT
+P07901	Hsp90aa1	RAFT
+P62245	Rps15a	RAFT
+P27659	Rpl3	RAFT
+Q9WU78	Pdcd6ip	RAFT
+Q6ZWU9	Rps27	RAFT
+P62259	Ywhae	RAFT
+P60335	Pcbp1	RAFT
+P84099	Rpl19	RAFT
+Q61753	Phgdh	RAFT
+P17225	Ptbp1	RAFT
+Q9D8N0	Eef1g	RAFT
+O70318	Epb41l2	RAFT
+P63101	Ywhaz	RAFT
+P57780	Actn4	RAFT
+P14131	Rps16	RAFT
+P18760	Cfl1	RAFT
+Q05144	Rac2	RAFT
+P29341	Pabpc1	RAFT
+P61979	Hnrnpk	RAFT
+Q9WTK5	Nfkb2	RAFT
+Q922D8	Mthfd1	RAFT
+P60867	Rps20	RAFT
+Q8VDN2	Atp1a1	RAFT
+Q8CGC7	Eprs	RAFT
+Q9CZD3	Gars	RAFT
+P62849	Rps24	RAFT
+P51912	Slc1a5	RAFT
+Q61233	Lcp1	RAFT
+Q9WUA3	Pfkp	RAFT
+Q07076	Anxa7	RAFT
+O35737	Hnrnph1	RAFT
+Q61881	Mcm7	RAFT
+P11440	Cdk1	RAFT
+P08101	Fcgr2	RAFT
+Q9JKF1	Iqgap1	RAFT
+O88207	Col5a1	RAFT
+P01900	H2-D1	RAFT
+P21995	Emb	RAFT
+P26041	Msn	RAFT
+P00405	Mtco2	RAFT
+P01837	UNKNOWN	RAFT
+Q9Z1Q9	Vars	RAFT
+O08807	Prdx4	RAFT
+Q60930	Vdac2	RAFT
+E9PVA8	Gcn1l1	RAFT
+P25918	Cd19	RAFT
+Q99LE6	Abcf2	RAFT
+Q921F2	Tardbp	RAFT
+P46935	Nedd4	RAFT
+P48962	Slc25a4	RAFT
+P53996	Cnbp	RAFT
+P00375	Dhfr	RAFT
+Q9D880	Timm50	RAFT
+P27546	Map4	RAFT
+O88569	Hnrnpa2b1	RAFT
+Q01853	Vcp	RAFT
+P10852	Slc3a2	RAFT
+P01863	Ighg	RAFT
+P62821	Rab1A	RAFT
+Q61470	Cd37	RAFT
+P35279	Rab6a	RAFT
+Q6ZQA6	Igsf3	RAFT
+Q02053	Uba1	RAFT
+P62196	Psmc5	RAFT
+P19096	Fasn	RAFT
+Q91V41	Rab14	RAFT
+P62960	Ybx1	RAFT
+P60229	Eif3e	RAFT
+P35278	Rab5c	RAFT
+O89053	Coro1a	RAFT
+Q8BGD9	Eif4b	RAFT
+Q9Z2X1	Hnrnpf	RAFT
+Q6A0D4	Rftn1	RAFT
+Q8BK64	Ahsa1	RAFT
+Q8VIJ6	Sfpq	RAFT
+P63094	Gnas	RAFT
+Q8R081	Hnrnpl	RAFT
+P20029	Hspa5	RAFT
+Q9QUI0	Rhoa	RAFT
+P53986	Slc16a1	RAFT
+Q61171	Prdx2	RAFT
+P62880	Gnb2	RAFT
+Q9D7G0	Prps1	RAFT
+P70372	Elavl1	RAFT
+Q8BTM8	Flna	RAFT
+Q60864	Stip1	RAFT
+P42932	Cct8	RAFT
+P10639	Txn	RAFT
+Q8VEM8	Slc25a3	RAFT
+Q01965	Ly9	RAFT
+Q9CW03	Smc3	RAFT
+P27601	Gna13	RAFT
+Q61598	Gdi2	RAFT
+P29351	Ptpn6	RAFT
+P21107	Tpm3	RAFT
+Q8BG05	Hnrnpa3	RAFT
+O09167	Rpl21	RAFT
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+Q8BT07	Cep55	RAFT
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diff --git a/examples/separate/CTT b/examples/separate/CTT
new file mode 100644
index 0000000..dd819b5
--- /dev/null
+++ b/examples/separate/CTT
@@ -0,0 +1,5 @@
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+P68134	Acta1	CTT
+P63001	Rac1	CTT
+Q60598	Cttn	CTT
+B9EJA2	Cttnbp2	CTT
diff --git a/negatome_mouse_pairs.tsv b/negatome_mouse_pairs.tsv
new file mode 100644
index 0000000..48c9f43
--- /dev/null
+++ b/negatome_mouse_pairs.tsv
@@ -0,0 +1,2171 @@
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diff --git a/patches/extraVerbose.patch b/patches/extraVerbose.patch
new file mode 100644
index 0000000..be20d60
--- /dev/null
+++ b/patches/extraVerbose.patch
@@ -0,0 +1,43 @@
+diff -pruN orig/caps.cpp new/caps.cpp
+--- orig/caps.cpp	2021-03-23 14:36:09.044861000 +0200
++++ new/caps.cpp	2021-03-23 17:21:39.432706915 +0200
+@@ -15,8 +15,8 @@
+ #include<sys/time.h>
+ #include<iomanip>
+ #include <bits/stdc++.h> 
+-
+-
++#include <vector>
++#include <string>
+ 
+ #include <Seq/SequenceApplicationTools.h>
+ #include <Seq/SiteTools.h>
+@@ -680,6 +680,10 @@ int main(int argc, char *argv[]){
+ 
+ 					threshold = totaltemp[value];
+ 					totaltempnew = totaltemp;
++					
++					// This is shamelessly taken from: https://stackoverflow.com/a/39746650
++					std::ofstream outFile("totaltemp.txt");
++					for (const auto &e : totaltemp) outFile << e << "\n";
+ 
+ 
+ 					/*=======================================================*/
+@@ -910,8 +914,6 @@ double getIndex(std::vector<double> cons
+ } 
+ 
+ 
+-
+-
+ /* 
+  * ===  FUNCTION  ======================================================================
+  *         Name:  print_inter
+@@ -926,7 +928,7 @@ int print_inter(vector<double>& Correl1,
+ 	int cor=0, pairs=0;
+ 
+ 	output << endl << endl;
+-
++	
+ 	output << "Coevolving Pairs of amino acid sites\n";
+ 	output << "================================================================================================================================\n";
+ 	output << "Col1(real)\tCol2(real)\tDmean1\t\tDmean2\t\tCorrelation\tBootstrap value\tP-value1\tP-value2\tMean P-value\tCorrelation1\tCorrelation2\n\n";
diff --git a/proteins/TLR b/proteins/TLR
new file mode 100644
index 0000000..cbe8cbd
--- /dev/null
+++ b/proteins/TLR
@@ -0,0 +1,4 @@
+Q9EPQ1	Tlr1	TLR
+Q9QUN7	Tlr2	TLR
+Q9QUK6	Tlr4	TLR
+Q9EPW9	Tlr6	TLR