     17    681

human                           CAG ACC AAT ATT GAT GTC GTG CCG TTC AAT GTC GCA GAA GGG AAG GAG GTC CTT CTA GTA GTC CAT AAT GAG TCC CAG AAT CTT TAT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG CAT GCC AAC TAT CGA ATT ATA GGA TAT GTA AAA AAT AGT CAA GAA AAT GCC CCA GGG CCC GCA CAC AAC GGT CGA GAG ACA ATA TAC CCC AAT GGA ACC CTG CTG ATC CAG AAC GTC ACC CAC AAT GAC GCA GGA ATC TAT ACC CTA CAC GTT ATA AAA GAA AAT CTT GTG AAT GAA GAA GTA ACC AGA CAA TTC TAC GTA TTC TCG GAG CCA CCC AAG CCC TCC ATC ACC AGC AAC AAC TTC AAT CCG GTG GAG AAC AAA GAT ATT GTG GTT TTA ACC TGT CAA CCT GAG ACT CAG AAC ACA ACC TAC CTG TGG TGG GTA AAC AAT CAG AGC CTC CTG GTC AGT CCC AGG CTG CTG CTC TCC ACT GAC AAC AGG ACC CTC GTT CTA CTC AGC GCC ACA AAG AAT GAC ATA GGA CCC TAT GAA TGT GAA ATA CAG AAC CCA GTG GGT GCC AGC CGC AGT GAC CCA GTC ACC CTG AAT GTC CGC TCA GTA CAA GCA AGT CCT GAC CTC TCA GCT GGG ACC GCT GTC AGC ATC ATG ATT GGA GTA CTG GCT GGG ATG GCT CTG ATA 
chimpanzee                      CAG ACC AAT ATT GAT GTC GTG CCG TTC AAT GTC GCA GAA GGG AAG GAG GTC CTT CTA GTA GTC CAT AAT GAG TCC CAG AAT CTT TAT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG CAT GCC AAC TAT CGA ATT ATA GGA TAT GTA AAA AAT AGT CAA GAA AAT GCC CCA GGG CCC GCA CAC AAC GGT CGA GAG ACA ATA TAC CCC AAT GGA ACC CTG CTG ATC CAG AAC GTC ACC CAC AAT GAT GCA GGA ATC TAT ACC CTA CAC GTT ATA AAA GAA AAT CTT GTG AAT GAA GAA GTA ACC AGC CAA TTC TAC GTA TTC TCG GAG CCA CCC AAG CCC TCC ATC ACC AGC AAC AAC TTC AAT CCG GTG GAG AAC AAA GAT ATT GTG GTT TTA ACC TGT CAA CCT GAG ACT CAG AAC ACA ACC TAC CTG TGG TGG GTA AAC AAT CAG AGC CTC CTG GTC AGT CCC AGG CTG CTG CTC TCC ATT GAC AAC AGG ACC CTC GTT CTA CTC AGC GCC ACA AAG AAT GAC ATA GGA CCC TAT GAA TGT GAA ATA CAG AAC CCA GTG GGT GCC AGC CGC AGT GAC CCA GTC ACC CTG AAT GTC CGC TCA GTA CAA GCA AGT CCT GAC CTC TCA GCT GGG ACC GCT GTC AGC ATC ATG ATT GGA GTA CTG GCT GGG ATG GCT CTG ATA 
bonobo                          CAG ACC AAT ATT GAT GTC GTG CCG TTC AAT GTC GCA GAA GGG AAG GAG GTC CTT CTA GTA GTC CAT AAT GAG TCC CAG AAT CTT TAT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG CAT GCC AAC TAT CGA ATT ATA GGA TAT GTA AAA AAT AGT CAA GAA AAT GCC CCA GGG CCT GCA CAC AAC GGT CGA GAG ACA ATA TAC CCC AAT GGA ACC CTG CTG ATC CAG AAC GTC ACC CAC AAT GAT GCA GGA ATC TAT ACC CTA CAA GTT ATA AAA GAA AAT CTT GTG AAT GAA GAA GTA ACC AGC CAA TTC TAC GTA TTC TCG GAG CCA CCC AAG CCC TCC ATC ACC AGC AAC AAC TTC AAT CCG GTG GAG AAC AAA GAT ATT GTG GTT TTA ACC TGT CAA CCT GAG ACT CAG AAC ACA ACC TAC CTG TGG TGG GTA AAC AAT CAG AGC CTC CTG GTC AGT CCC AGG CTG CTG CTC TCC ATT GAC AAC AGG ACC CTC GTT CTA CTC AGC GCC ACA AAG AAT GAC ATA GGA CCC TAT GAA TGT GAA ATA CAG AAC CCA GTG GGT GCC AGC CGC AGT GAC CCA GTC ACC CTG AAT GTC CGC TCA GTA CAA GCA AGT CCT GAC CTC TCA GCT GGG ACC GCT GTC AGC ATC ATG ATT GGA GTA CTG GCT GGG ATG GCT CTG ATA 
gorilla                         AAG CTC ACT ATT GAA TCC ACG CCG TTC AAT GTC GCA GAA GGG AAG GAG GTC CTT CTA CTA GTC CAT AAT GAG TCC CAG AAT CTT TAC GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG CAT GCC AAC TAT CGA ATT ATA GGA TAT GTA AAA AAT AGT CAA GAA AAT GCC CCA GGG CCC GCA CAC AAC GGT CGA GAG ACA ATA TAC CCC AAT GGA TCC CTG CTG ATC CAG AAC GTC ACC CAC AAT GAC GCA GGA ATC TAT ACC CTA CAG GTT ATA AAA GAA AAT CTT GTG AAT GAA GAA GTA ACC AGC CAA TTC TAC GTA TTC TCG GAG CCA CCC AAG CCC TCC ATC ACC AGC AAC AAC TTC AAT CCG GTG GAG AAC AAA GAT ATT GTG GTT TTA ACC TGT CAA CCT GAG ACT CAG AAC ACA ACC TAC CTG TGG TGG GTA AAC AAT CAG AGC CTC CTG GTC AGC CCC AGG CTG CTG CTC TCC ACT GAC AAC AGG ACC GTC GTT CTA CTC AGC GCC ACA AAG AAT GAC ATA GGA CCC TAT GAA TGT GAA ATA CAG AAC CCA GTG GGT GCC AGC CGC AGT GAC CCA GTC ACC CTG AAT GTC CGC TCA GTA CAA GCA AGT CCT GAC CTC TCA GCT GGG ACC GCT GTC AGC ATC ATG ATT GGA GTA CTG GCT GGG ATG GCT CTG ATA 
orangutan                       CAG ACC ACT ATT GAA GTC GTG CCG TTC AAT GTC GCA GAA GGG AAG GAG GTC CTT CTA CTA GTC CAT AAT GAG TCC CAG AAT CTT TAT GGC TAC AAC TGG TAC AAA GGG GAA ACG GTG CAT GCC AAC TAT CGA ATT ATA GGA TAT GTA CAA AAT AGT CAA GAA AAT GCC CCA GGG CCC GCA CAC AAC GGT CGA GAG ACA ATA TAC CCC AAT GGA TCC CTC CTG ATC CAG AAC GTC ACC CAC AAT GAC GCA GGA ATC TAT ACC CTA CAA GTT ATA AAA GAA AAT CTT AAC AGT GAA GAA GTA ACC AGC CAA TTC TAC GTA TTC TCG GAG CCA CCC AAG CCC TCC ATC ACC AGC AAC AAC TTC AAT CCG GTG GAG AAC GAG GAT ATT GTG GTT TTA ACC TGT CAA CCT GAG ACT CAG AAC ACA ACC TAC CTG TGG TGG GTA AAC AAT CAG AGC CCC CTG GTC AGT CCC AGG CTG CTG CTC TCC ACT GAC AAC AGG ACC CTC ATT CTA CTC AAC GTC ACA AAG AAT GAC ATA GGA CCC TAT GAA TGT GAA ATA CAG AAC CCA GTG GGT GCC AGC CGC AGT GAC CCA GTC ACC CTG AAT GTC CGC TCA GTA CAA GCA AGT CCT GAC CTC TCA GCT GGG ACC GCT GTC AGC ATC ATG ATT GGA GTA CTG GCT GGG ATG GCT CTG ATA 
colobus                         CAG ACT ATC AGT GAA GTC GTG CCG TTC AAT GTT GCA GAG GGG AAG GAG GTC ATT CTG CTA GTC CAT AAT GTG TCC CAG AAT CTT TAT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG CAC GCC AAC TAT CGA ATT ATA GGA TAT GTA ATA AAC CGT GGA GAA AAT GCC CCA GGG CCC GCA CAC AGC GGT CGA GAG ACA ATA TAC CCT AAT GGA TCC CTG CTG ATC CAG AAC GTC AAC CTC AAT GAC CCA GGA ATC TAT ACC CTA CAC GTT ATA AAC AGA GAT CTT GTG AAT GAA GAA GTA ACT AGC CAA TTC TAC GTA TTC CCG GAA CCA CCA AAG CCC TCC ATC TCC AGC AAC AAC TTC AAT CCG GTG GAG AAC AAG GAT ATT GTG GTT TTA ACC TGT CAA CCT GAA ACT CAG GAC ACA ACC TAT CTA TGG TGG GTA AGC AAT CAG AGC CTC CAG GTC AGT CCC AGG CGG CTG CTC TCC ATT GAC AAC AGG ACC CTC GTT CTA CTG AGT GTC ACA AGG AAT GAG AAA GGA CCC TAT GAA TGT GAA ATA CAG AAC CCA GTG GGT GCC AGG CGC AGT GAC CCT GTC ACC CTG AAT GTT CGC TCA GTA CCA GGA AGT CCT GAC CTC TCA GCT GGG ACT GCT GTC AGT ATC ATG ATT GGA GTA CTG GCT GGG ATT GCT CTA ATA 
AGM                             CCG ACT AAC ATT GAA GTT GTG CCG TTC AAT GTT GCA GAG GGG AAG GAG GTC ATT CTG CTA GTC AGT AAT GTG TCC CAC AAT CTT TAT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG CAT GCC AAC TAT CGA ATT ATA GGA TAT GTA ACA AAC AAA GGA GAA ACT GCT CCA GGG CCC GCA CAC AGT GGT CGA GAG ACA ATA TAC CCC AAT GGA TCC CTG CTG ATC CAG AAC GTC AGC CTC AAC GAC CCA GGA ATC TAT ACC CTA CAC GTT ATA AAT GAA GAT CTT GTG AAT GAA GAA GTA ACC AGG CAA TTC TAC GTA TTC TCG GAG CCA CCA AAG CCC TCC ATC TCC AGC AAC AAC TTC AAT CCG GTG GAG AAC AAG GAT ATT GTG GCT TTA ACC TGT CAA CCT GAA ACT CAG GAC ACA ACC TAC CTG TGG TGG GTA AAC AAT CAG AGC CTC CAG GTC AGT CCC AGG CGG CTG CTC TCC ATT GAC AAC AGG ACC CTC GTT CTA CTG AGC GTC ACA ATG AAT GAC AAA GGA CCC TAT GAA TGT GAA ATA CAG AAC CCA GTG GGT GCC AGG CGC AGT GAC CCA GTC ACC CTG AAT GTC CGC TCA GTA CCA GGA AGT CCT GAC CTC TCA GCT GGG ACC GCT GTC AGC ATA ATG ATT GGA GTA CTG GCT GGG ATG GCT CTG ATA 
baboon                          CAG ACT AAC ATT GAA GTT GTG CCG TTC AAT GTT GCA GAG GGG AAG GAG GTC ATT CTG CTA GTC AGT TAT GTG TCC CGC AAT CTT TAT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG CAC GCC AAC TAT CGA ATT ATA GGA TAT GTA GTA AAC CAA GGA GAA AAT GCC CCA GGG CCC GCA CAC AGC GGT CGA GAG ACA ATA TAC TCC AAT GGA TCC CTG CTG ATC CAG AAC GTC GGC CTC AGT GAC CCA GGA ATC TAT ACC CTA CAC GTT ATA AGC GAA GAT CTT GTG ACT GAA GAA GTA ACC AGG CAA TTC TAC GTA TTC TCG GAG CCA CCA AAG CCC TCC ATC TCC AGC AAC ACC TTC AAT CCG GTG GAG AAC AAG GAT ATT GTG GCT TTA ACC TGT CAA CCT GAA ACT CAG GAC ACA ACC TAC CTG TGG TGG GTA AAC AAT CAG AGC CTC CAG GTC AGT CCC AGG CGG CTG CTC TCC GTT GAC AAC AGG ACC CTC GTT CTA CTG AGC GTC ACA ACG AAT GAC AAA GGA CCC TAT GAA TGT GAA ATA CAG AAC CCA GTG GGT GCC AGG CGC AGT GAC CCA GTC ACC CTG AAT GTC CGC TCA GTA CCA GGA AGT CCT GAC CTC TCA GCT GGG ACC GCT GTC AGC CTC ATG ATT GGA GTA CTG GCT GGG ATG GCT CTG ATA 
sootyM                          CAG ACT AAC ATT GAA GTT GTG CCG TTC AAT GTT GCA GAG GGG AAG GAG GTC ATT CTG CTA GTC AGT AAT GTG TCC CGC AAT CTT TAT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG CAC GCC AAC TAT CGA ATT ATA GGA TAT GTA ATA AAC CAA GGA GAA AAT GCC CCA GGG CCC GCA CAC AGT GGT CGA GAG ACA ATA TAC TCC AAT GGA TCC CTG CTG ATC CAG AAC GTC GGC CTC AGT GAC CCA GGA ATC TAT ACC CTA CAC GTT ATA AGC GAA GAT CTT GTG ACT GAA GAA GTA ACC AGG CAA TTC TAC GTA TTC TCG GAG CCA CCA AAG CCC TCC ATC TCC AGC AAC ACC TTC AAT CCG GTG GAG AAC AAG GAT ATT GTG GCT TTA ACC TGT CAA CCT GAA ACT CAG GAC ACA ACC TAC CTG TGG TGG GTA AAC AAT CAG AGC CTC CAG GTC AGT CCC AGG CGG CTG CTC TCC GTT GAC AAC AGG ACC CTC GTT CTA CTG AGC GTC ACA ACG AAT GAC AAA GGA CCC TAT GAA TGT GAA ATA CAG AAC TCA GTG GGT GCC AGG CGC AGT GAC CCA GTC ACC CTG AAT GTC CGC TCA GTA ACA GGA AGT CCT GAC CTC TCA GCT GGG ACC GCT GTC AGC ATC ATG ATT GGA GTA CTG GCT GGG ATG GCT CTG ATA 
CEmac                           CAG ACT AAC ATT GAA GTT GTG CCG TTC AAT GTT GCA GAG GGG AAG GAG GTC ATT CTG CTA GTC AGT AAT GTG TCC CGC AAT CTT TAT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG CAC GCC AAC TAT CGA ATT ATA GGA TAT GTA ACA AAC AAA GGG GAA AAT GCC CCA GGG CCT GCA CAC AGT GGT CGA GAG ACA ATA CAC CGC AAC GGA TCC CTG CTG ATC CAG AAC GTC AGC CTC AGT GAC CCA GGA ATC TAT ACC CTA CAC GTT ATA AGC GAA GAT CTT GTG ACT GAA GAA GTA ACC AGG CAA TTC TAC GTA TTC TCG GAG CCA CCA AAG CCC TCC ATC TCC AGC AAC ACC TTC AAT CCG GTG GAG AAC AAG GAT ATT GTG GCT TTA ACC TGT CAA CCT GAA ACT CAG GAC ACA ACC TAC CTG TGG TGG GTA AAC AAT CAG AGC CTC CAG GTC AGT CCC AGG CGG CTG CTC TCC GTT GAC AAC AGG ACC CTC GTT CTA CTG AGC ATC ACA ACA AAT GAC AAA GGA CCC TAT GAA TGT GAA ATA CAG AAC CCA GTG GGT GCC AGG CGC AGT GAC CCA GTC ACC CTG AAT GTC CGC TCA GTA CCA GGA AGT CCT GAC CTC TCA GCT GGG ACC GCT GTC AGC ATC ATG ATT GGA GTA CTG GCT GGG ATG GCT CTG ATA 
rhesus                          CAG ACT AAC ATT GAA GTT GTG CCG TTC AAT GTT GCA GAG GGG AAG GAG GTC ATT CTG CTA GTC AGT AAT GTG TCC CGC AAT CTT TAT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG CAC GCC AAC TAT CGA ATT ATA GGA TAT GTA ACA AAC AAA GGG GAA AAT GCC CCA GGG CCT GCA CAC AGT GGT CGA GAG ACA ATA CAC CGC AAC GGA TCC CTG CTG ATC CAG AAC GTC AGC CTC AGT GAC CCA GGA ATC TAT ACC CTA CAC GTT ATA AGC GAA GAT CTT GTG ACT GAA GAA GTA ACC AGG CAA TTC TAC GTA TTC TCG GAG CCA CCA AAG CCC TCC ATC TCC AGC AAC ACC TTC AAT CCG GTG GAG AAC AAG GAT ATT GTG GCT TTA ACC TGT CAA CCT GAA ACT CAG GAC ACA ACC TAC CTG TGG TGG GTA AAC AAT CAG AGC CTC CAG GTC AGT CCC AGG CGG CTG CTC TCC GTT GAC AAC AGG ACC CTC GTT CTA CTG AGC ATC ACA ACG AAT GAC AAA GGA CCC TAT GAA TGT GAA ATA CAG AAC CCA GTG GGT GCC AGG CGC AGT GAC CCA GTC ACC CTG AAT GTC CGC TCA GTA CCA GGA AGT CCT GAC CTC TCA GCT GGG ACC GCT GTC AGC ATC ATG ATT GGA GTA CTG GCT GGG ATG GCT CTG ATA 
PTmac                           CAG ACT AAC ATT GAA GTT GTG CCG TTC AAT GTT GCA GAG GGG AAG GAG GTC ATT CTG CTA GTC AGT AAT GTG TCC CGC AAT CTT TAT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG CAC GCC AAC TAT CGA ATT ATA GGA TAT GTA ATA AAC AAA GGG GAA AAT GCC CCA GGG CCT GCA CAC AGT GGT CGA GAG ACA ATA CAC CGC AAC GGA TCC CTG CTG ATC CAG AAC GTC AGC CTC AGT GAC CCA GGA ATC TAT ACC CTA CAC GTT ATA AGC GAA GAT CTT GTG ACT GAA GAA GTA ACC AGG CAA TTC TAC GTA TTC TCG GAG CCA CCA AAG CCC TCC ATC TCC AGC AAC ACC TTC AAT CCG GTG GAG AAC AAG GAT ATT GTG GCT TTA ACC TGT CAA CCT GAA ACT CAG GAC ACA ACC TAC CTG TGG TGG GTA AAC AAT CAG AGC CTC CAG GTC AGT CCC AGG CGG CTG CTC TCC GTT GAC AAC AGG ACC CTC GTT CTA CTG AGC ATC ACA ACG AAT GAC AAA GGA CCC TAT GAA TGT GAA ATA CAG AAC CCA GTG GGT GCC AGG CGC AGT GAC CCA GTC ACC CTG AAT GTC CGC TCA GTA CCA GGA AGT CCT GAC CTC TCA GCT GGG ACC GCT GTC AGC ATC ATG ATT GGA GTA CTG GCT GGG ATG GCT CTG ATA 
drill                           CAG ACT AAC ATT GAA GTT GTG CCG TTC AAT GTT GCA GAG GGG AAG GAG GTC ATT CTG CTA GTC AGT AAT GTG TCC CGC AAT CTT TAT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG CAC GCC AAC TAT CGA ATT ATA GGA TAT GTA ACA AAC AAA GGG GAA AAT GCC CCA GGG CCC GCA CAC AGC GGT CGA GAG ACA ATA TAC TCC AAT GGA TCC CTG CTG ATC CAG AAC GTC AGC CTC AGT GAC CCA GGA ATC TAT ACC CTA AAC GTT ATA AAC GAA GAT CTT GTG AAT GAA GAA GTA ACC AGG CAA TTC TAC GTA TTC TCG GAG CCA CCA AAG CCC TCC ATC TCC AGC AAC ACC TTC AAT CCG GTG GAG AAC AAG GAT ATT GTG GCT TTA ACC TGT CAA CCT GAA ACT CAG GAC ACA ACC TAC CTG TGG TGG GTA AAC AAT CAG AGC CTC CAG GTC AGT CCC AGG CGG CTG CTC TCC ATT GAC AAC AGG ACC CTC GTT CTA CTG AGC GTC ACA ACG AAT GAC AAA GGA CCC TAT GAA TGT GAA ATA CAG AAC TCA GTG GGT GCC AGG CGC AGT GAC CCA GTC ACC CTG AAT GTC CGC TCA GTA ACA GGA AGT CCT GAC CTC TCA GCT GGG ACC GCT GTC AGC ATC ATG ATT GGA GTA CTG GCT GGG ATG GCT CTG ATA 
capuchin                        CAG CTC AGT ACT GAA GCT GTG CCA CCC ATT GTC GCA GAG GGG AAG GAG GTT CTT CTG CTT GTC CAC AAC CTG CCC CAG GAC CCT CTT GGC TAC AAC TGG TAC AAA GGG GAA ATG GTG GAT GCC AAA CAG CGA ATT ATA GGA TAT GTA GTG AGA TCT CAA ATA ACT ACC CCA GGG CCC GCA TAC AGC GGT CGA GAG ACA GTG TAC CCC AAT GCA TCC CTG CTG ATC CAG AGC GTC ACC CCA AAT GAC ACA GGA AGC TAC ACC CTA CAG GTC ATA GAC ACA AAT CTT ACG AAT GAG GAA GTA CTC GGC CGA TTC GAT GTG CAG GCG GAG CCG CCC AAG CCC TAC ATC ACC AGC AAC AAC TTC AAC CCC GTG GAG AAC AAG GAT GTT GTG GCC TTA ACC TGT GAA CCT GAG ACT CAG AAC ACA ACC TAC CTG TGG TGG GTG AAC AAT CAG AGC CTC CCG GTC AGT CAC AGG CTG GTG CTC TCC GGT GAC AAT AGG ACC CTC ATT CTA CTC AGT GTC ACA AGG AAT GAC AGA GGA CCC TAT GAG TGT GAA ATA CAG AAC ACA CTG AGT GCC AGC CGC AGT GAC CCA GTC ACC CTG AAT GTT CGC TCA GTA CCA GAC AGT TCT GTT GTC TCA GCT GGG ACC ACT GTC AGC ATC ATG ACT GGA GTG CTG GCC GCG GTG GCT CTC ACA 
squirrelM                       CAG CCC AGC ATT GAA GCT GTG CCA CCC ATT GTT GCA GAG GGG AAG GAG GTT CTT CTG CTT GTC CAT AAC ATG TCC CAA GAT CTT ATT GGC TAC AAC TGG TAC AAA GGA GAA AGG GTG GAC GCC AAC TAT CGA ATT ATA GGA TAT GTA GCA AGT TCT CAA GAA TCT CCA CCA GGG CCC GCA TAC AGC AAT CGA GAG ACA CCG TAC CCC AAT GGA TCC CTG CTG ATC CAG AGC ATC ACC CCC AAT GAC ACA GGA AGC TAC ACC CTA CAG GTC ATA GAC ACA AAT CTT ACG AGT GAA GAA GTA CTT GGC CGA TTC GAC GTG CAG GCG GTG CCA CCC AAG CCC TAC ATC ACC AGC AAC AAC TTC AAC CCC GTT GAG AAC AAG GAT GTT GTG GCT TTA ACC TGT GAA CCT GAG ACT CAG GAC ACA ACC TAC CTG TGG TGG GTG AAC AAT CAG AGC CTC CCG GTC AGT TCC AGG CTG GTG CTC TCC AGT GAC AAC AGG ACC CTC ATT CTA CTT AGT GTC ACA AGG AAT GAC ACA GGA CCC TAT GAG TGT GAA ATA CAG AAC CTA GTG AGT GCC AGC CAC AGT GAC CCA GTC ACC CTG AAT GTC CGC CCA GTA CCA GAC AGT CCT GTT GTC TCA GCT GGG ACC ACT GCC AGC ATC ATG ACT GGA GTG CTG GCT GGG GTG GCT CTG ATA 
nightM                          CAG CCC AGT ATT GAA GCC GTG CCA CCC CTT GTC GCA GAG GGG AAG GAG GTT CTT CTG CTA GCC CAT AAC GTG TCC CAA GAT CTT TTT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG GCC GCC AAC TAT CGA ATT ATA GGA TAC AGA ATA GAG AGT CAA GTA TCT ACC ACA GGG CCC GCA TAC AGC GGT CGA GAG ACA CTG TAC CCC AAT GGA TCC CTG CTG GTC CAG AGC GTC ACC CCC AAT GAC ACA GGA AGC TAC ACC CTA CAC CTC ATA GAC AGA AAC ATT ACA GGT GAA GAA GTA CTC GGC CGA TTC GAC GTG CAG GCG GCG CCG CCC AAG CCC TAC ATC ACC AGC AAC AAC TTC AAC CCC ATA GAG AAC AAG GAT GTT GTG GCT TTA ACC TGT GAA CCT GAG ACT CAG AAC ACA ACC TAC CTG TGG TGG GTG AAC AAT CAG AGC CTC CCG GTC AGT TCC AGG CTG GTG CTC TCC AGT GAC AAC AGG ACC CTC GTT CTC ATC AGT GTC ACA AGG AAT GAC ACA GGA CCC TAT GAA TGT GAA ATA CAG AAC ACA CTG AGT GCC AGC CGC AGC GAC CCA GTC ACC CTG CTT GTC CGC TCA GTA CCA GAT AGT CCT GTC CTC TCA GCT GGG ACC ACT GTC AGC ATG ATG ACT GGA GTG CTG GCC GCG ATG GCT CTG ATA 
marmoset                        CAG CCC AGT ATT GAA GCC GTG CCA CCC ATT GTT GGG GAG GGG AAG GAG GTT CTT CTG CTT GTC AAT AAC ATG TCC CAA GAT GTT TTT GGC TAC AAC TGG TAC AAA GGG GAA AGG GTG GAC AGC AAC TAT CGG ATT ATA GGA TAT GCA ATA GAG ACT CAA GTA TCT ACC TCA GGG CCG GCA CAC AGC GGC CGG GAG ATA TTG TTC CCC AGT GCA TCC CTG CTG ATC CAG AGC GTC ACC CCC AGC GAC ACA GGA AGC TAC ACC CTA CAC GTC ATA CAC AGA AAC CTT ACG AGC GAA GAA GTA TTC GGC CGA TTC GAC GTG CAG GCG GCG CTG CCC AAG CCC TAC ATC ACC AGC AAC AAC TTC AAC CCC GTG GAG AAC GAG GAT GTT GTG GCT TTA ACC TGT GAA CCT GAG ACT CAG AAC ACA ACC TAC CTG TGG TGG GTG AAC AAT CAG AGC CGC CCC GTC AGT TCC AGG CTG GTG CTC TCC AGT GAC AAC AGG ACC CTC ATT CTA ATC AGT GTC ACA AGG AAT GAC ACA GGA CCC TAT GAA TGT GAA ATA CAG AAC ACA CTG AGT GCC AGC CGC AGC GAC CCA GTC ACC CTC AAT GTC CGC TCA GTA TCA GGC GGT CCT GTT GTC TCA GCT GGG ACC ACT GTC AGC ATC ATG ACT GGA GTG CTG GCT GGG GTG GCT CTG ATA 



Printing out site pattern counts


        17        558  P

human                           AAA AAA AAA AAA AAC AAC AAC AAC AAC AAC AAC AAC AAG AAG AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACA ACA ACC ACC ACC ACC ACC ACC ACC ACT ACT AGA AGC AGC AGC AGC AGG AGG AGT AGT AGT AGT ATA ATA ATA ATA ATC ATC ATC ATC ATG ATG ATT ATT ATT ATT CAA CAA CAA CAA CAC CAC CAC CAG CAG CAG CAT CAT CCA CCA CCA CCA CCC CCC CCC CCC CCC CCG CCG CCT CCT CGA CGC CGC CTA CTA CTA CTC CTC CTC CTC CTC CTG CTG CTG CTG CTG CTG CTG CTG CTT CTT CTT GAA GAA GAA GAA GAA GAA GAC GAC GAC GAC GAG GAG GAG GAG GAT GAT GCA GCA GCA GCA GCC GCC GCC GCC GCT GCT GCT GGA GGA GGC GGG GGG GGG GGT GGT GTA GTA GTA GTA GTC GTC GTC GTC GTC GTC GTC GTC GTG GTG GTG GTG GTG GTT GTT GTT TAC TAC TAC TAC TAT TAT TAT TAT TAT TCA TCA TCC TCC TCC TCG TGG TGT TTA TTC TTC TTC 
chimpanzee                      ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
bonobo                          ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
gorilla                         ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... ... ... ... ... CT. T.. ... ... ..C ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... TC. AC. ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
orangutan                       ... ... C.. G.G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. .C. ... ... ... ... ... ... ... ... T.. ... ... ..C .A. ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... AAC ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
colobus                         ... ..C .T. ..G ... ... ... ... ... .G. .G. G.. ... .G. ..C ... ... ... ... ... ... ... ... ... G.. ... .TC ... ... .A. ... ..T ..T T.. ..T T.. ... .T. ..C ..T ... ..G ..T ... ... ... ... ... C.. .A. ... ... ... ... ... ... ... ... ..T .G. ... ... ... ... ... .C. GG. ... ... .T. ... ... ... ..C ... ... ... ... ..T ..A ... ... ..T ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ..G ... ... .A. .G. ..A ..A ... ... ... A.. ... ... AG. ... ... ... ... ..G ... ... ..G ... ..A ..A ... .T. ..A ... C.. ... ... .G. ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ..T ..T ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... 
AGM                             ... ..T .C. ..G ... ... ... ... ... ... .GT G.. ... .T. ..C ..C ... ... ... ... ... ... ... .C. G.. ... ..C ... ... .G. ... ... ... T.. ..T T.. ... .T. ..G ... ... ..G ... ... ... ... ... ... .AA .A. ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... .C. GG. ... ... .T. .C. ..C ... ... AG. ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ..G ... ... .A. .G. ... ... ... ... ... A.. ... ... ... ... ... ... ... ..G ... ... ... ... ..A ... ... .T. ..A ... C.. ... ... .G. ... ... ..T .T. ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ..T ..T ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
baboon                          ... .GC GT. ..G ... ... ... ... .C. ... .G. G.. ... .C. ..C .G. ... ... ... ... ... ... T.. ... G.. .C. ..C ... ... GG. ... ... ... T.. ..T T.. ... GT. ..G ... ... ..G ... ... ... ... ... ... CAA .A. ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... .C. GG. ... ... .T. ... .GC ... ..C AG. ... ... ... ... ..A ... ... T.. ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ..G ... ... .A. .G. ... ... ... ... ... A.. ... ... ... ... ... ... ... ..G ... ... ... ... ..A ... ... .T. ..A ... C.. ... ... .G. ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ..T ..T ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
sootyM                          ... .GC .T. ..G ... ... ... ... .C. ... .GT G.. ... .C. ..C .G. ... ... ... ... ... ... ... ... G.. .C. ..C ... ... GG. ... ... ... T.. ..T T.. ... GT. ..G ... ... ..G ... ... ... ... ... ... CAA .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... AC. GG. ... ... .T. ... .GC ... ..C AG. ... ... T.. ... ..A ... ... T.. ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ..G ... ... .A. .G. ... ... ... ... ... A.. ... ... ... ... ... ... ... ..G ... ... ... ... ..A ... ... .T. ..A ... C.. ... ... .G. ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ..T ..T ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
CEmac                           ... .GC .C. ..G ... ... ... ... .C. ... .GT G.. ... .CA ..C .G. ..C ... ... ... ... ... ... ... G.. .C. ..C ... ... .G. ... ... ... T.. ..T T.. ... GT. ..G ... ... ..G ... ... ... ... ... ... .AA .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. GGG ... ... .T. ... .GC ... ..C AG. ... ... ... ... ..A ... ... .G. ..T ... ... ... ... ... ... ... ... ... ..G ... ... ... ..G ... ... .A. .G. ... ... ... ... ... A.. ... ... ... ... ... ... ... ..G ... ... ... ... ..A ... ... .T. ..A ... C.. ... ... .G. ... ... ... AT. ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ..T ..T ... ... ... ... ... ... .C. ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
rhesus                          ... .GC .C. ..G ... ... ... ... .C. ... .GT G.. ... .C. ..C .G. ..C ... ... ... ... ... ... ... G.. .C. ..C ... ... .G. ... ... ... T.. ..T T.. ... GT. ..G ... ... ..G ... ... ... ... ... ... .AA .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. GGG ... ... .T. ... .GC ... ..C AG. ... ... ... ... ..A ... ... .G. ..T ... ... ... ... ... ... ... ... ... ..G ... ... ... ..G ... ... .A. .G. ... ... ... ... ... A.. ... ... ... ... ... ... ... ..G ... ... ... ... ..A ... ... .T. ..A ... C.. ... ... .G. ... ... ... AT. ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ..T ..T ... ... ... ... ... ... .C. ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
PTmac                           ... .GC .T. ..G ... ... ... ... .C. ... .GT G.. ... .C. ..C .G. ..C ... ... ... ... ... ... ... G.. .C. ..C ... ... .G. ... ... ... T.. ..T T.. ... GT. ..G ... ... ..G ... ... ... ... ... ... .AA .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. GGG ... ... .T. ... .GC ... ..C AG. ... ... ... ... ..A ... ... .G. ..T ... ... ... ... ... ... ... ... ... ..G ... ... ... ..G ... ... .A. .G. ... ... ... ... ... A.. ... ... ... ... ... ... ... ..G ... ... ... ... ..A ... ... .T. ..A ... C.. ... ... .G. ... ... ... AT. ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ..T ..T ... ... ... ... ... ... .C. ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
drill                           ... ..C .C. ..G ... ... ... ... .C. ... .G. G.. ... .C. ..C .G. ... ... ... ... ... ... ... ... G.. ... ..C ... ... .G. ... ... ... T.. ..T T.. ... .T. ..G ... ... ..G ... ... ... ... ... ... .AA .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... AC. GGG A.. ... .T. ... .GC ... ..C AG. ... ... T.. ... ..A ... ... T.. ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ..G ... ... .A. .G. ... ... ... ... ... A.. ... ... ... ... ... ... ... ..G ... ... ... ... ..A ... ... .T. ..A ... C.. ... ... .G. ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ..T ..T ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
capuchin                        ... G.C GTG ..G ..A ... ..T .G. ... ... .G. ... ... .G. .GA ... ... ..C ... ... .T. G.C ..C .C. ... ... .G. ... ... ... ... ... CT. ... CT. T.. ... GG. G.C ..T ... ... ... .T. ... ... ... ... TC. .G. .C. ... G.G ... .G. ... ... ... G.. .C. .C. ... G.. .G. G.. .C. ... ..G T.. .CA ... ... ... G.. ..C ... ..G A.. ... ... .A. ... ... ... ..A ..C ... T.. ... ... ... ... ... ..G ... ... G.. ... ... ... .C. ... ..C ... ... ... G.. ... .C. ... AC. AT. ... ..G ..G ..G ... .TT ... ... ... ... ... CT. ..A ... A.. ... ... .AC ... ... A.. .T. A.. ..C ... .C. ... ... .C. ... ... A.. ... C.T ... ... ..G ... ... ... ... ..T ..T ... .CT ... AC. C.. ... ... A.. .CC ..C ... G.T ... ... CT. C.G ..C ... ... ... ... C.. .A. ... G.. ... ... ... CAG CC. ... 
squirrelM                       ... G.C GC. ..G ... ... ... .G. ... ... .G. G.. ... .G. .G. ... ... ..C ... ... .T. G.. ..C TC. ... .G. .GC ... ... ... ... ... CTT ... C.. T.. ... .G. G.C ..T ... ... ... ... ... ... ... ... TC. .C. ... ... CCG ... .G. ... ... ... G.. ... .C. ... G.. .G. G.. .C. ... ..G T.. .C. ... ..A ... G.C ... ... ... .T. ... ... T.. ... ... ... ..A ..C ... ... ... .A. ... ... ... ..G ... ... G.. ..T ... ... .C. ... ... ... ... ... G.. ... ... ... AC. ... ... ... ..G ..G ... .TT ... ... ... .T. ... AT. ..A ... A.. ... ... .AC ... ... C.A .T. A.. ... ... ... ... ... ... ..A ... A.. AA. C.T ... ... ..G A.. .C. ... ... ..T ... ..T .CT ... AC. ... ... ..T A.. .C. ..C ... G.. ... ... AT. ... ..C ... ... C.. ... ... .A. ... G.. ... ... ... CAG CC. ... 
nightM                          ... G.C .T. ..G ... ... ... .G. ... ... .G. ... ... .G. G.G ... ... ..C ... CT. CT. G.. ..C TC. ..C GG. .G. ... ... ... ... ... CT. ... C.. T.. ... .G. G.C ..T ... ... ... ... ... ... ..C ... ... .C. ... ... C.G ..G .G. ... G.. ... ... ... .C. ... G.. .G. G.. .C. ... ... T.. .C. ... ..A ... GCC ... A.. ..G A.. ... ... T.. ... ... ... ..A ..C ... ... ... ... ... ... ..C ..G ... ... ... A.. ... ... .C. ... ... ... ... ... G.. ... ... A.. AG. .T. ... ... ... ..G ... .T. ... ... ... .C. ... .T. ..A ... A.. ... ... .AT ... ... A.. .T. A.. ..C ... ... ... ... .C. ... ... A.. ... C.. AG. ... ..G ... ... .C. ... ..T ... ... .C. ... ACA C.. ... A.A ... .C. C.C ... G.. ... ... .T. ... ..C ..C ... ... ... ... .A. ... G.. ... ... ... CAG CC. ... 
marmoset                        ... C.C .T. G.G ... ... ... .G. ... ... .G. ... ... .G. G.G .GC .G. ..C ... ... .T. G.. ..C TC. ..C .GC .G. ... .T. ... ... ... TT. ... C.. T.. ... .G. G.C ..T ... ... ... ... ... ... ..C G.. .C. .C. ... ... T.G ... .G. ... ... ... G.. ... .C. ... G.. .G. G.. TC. ... ... ... .C. ... ..A ... G.C A.. T.. .TG A.. ... ... T.. ... ... ..G ..A ..C ... ... ..G ... ... ... ... ..G .G. ... G.. A.. ... ... .CC ... ... ... ..C ... G.. ... G.. ... AG. .T. ... ... ... ..G ... .TT ... ... ... .C. ... AT. ..A ... A.. ... .GG .GC AG. ... A.. .T. A.. ... ... .C. ... ... ... ... ... A.. ..C C.T .C. ... ..G ... ... ... ... ..T ... ..T .C. ... AC. C.. ... ... A.. .C. ..C .T. G.. ... ... .T. ... ..C ... ... ... ... ... .A. ... G.. ... ... ... CAG CC. ... 

    1    1    1    1    1    4    1    1    1    1    1    1    2    1    1
    1    1    1    2    1    1    1    1    1    1    1    1    2    1    1
    5    1    1    1    1    1    1    1    1    1    2    1    1    1    2
    1    1    1    1    1    1    3    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    4    1    1
    1    1    1    1    1    1    2    1    1    1    1    1    1    2    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    2    1    1    1    1    1    1    3    1    1    1    2    1    1    1
    1    1    3    1    1    1    1    1    1    1    1    1    1    1    1
    1    2    1    4    1    1    1    3    1    1    1    1    2    3    1
    1    1    2    1    1    1    1    1    1    1    2    1    1    1    1
    1    1    2    1    1    1    1    1    1    1    1    1    1    1    1
    3    2    1    1    1    2

CODONML (in paml version 4.9h, March 2018)  CEACAM7seq.txt
Model: One dN/dS ratio, 
Codon frequency model: F3x4
Site-class models: 
ns =  17  ls = 227

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   0   0   0   0   0   0 | Ser TCT   0   0   0   0   0   0 | Tyr TAT   5   5   5   4   5   6 | Cys TGT   2   2   2   2   2   2
    TTC   4   4   4   4   4   4 |     TCC   3   3   3   5   4   5 |     TAC   5   5   5   6   5   4 |     TGC   0   0   0   0   0   0
Leu TTA   1   1   1   1   1   1 |     TCA   2   2   2   2   2   2 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
    TTG   0   0   0   0   0   0 |     TCG   1   1   1   1   1   0 |     TAG   0   0   0   0   0   0 | Trp TGG   3   3   3   3   3   3
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   3   3   3   3   3   2 | Pro CCT   2   2   3   2   2   4 | His CAT   2   2   2   2   2   1 | Arg CGT   0   0   0   0   0   1
    CTC   5   5   5   5   5   5 |     CCC   6   6   5   6   7   4 |     CAC   3   3   2   2   2   3 |     CGC   2   2   2   2   2   2
    CTA   3   3   3   4   4   5 |     CCA   4   4   4   4   4   6 | Gln CAA   4   4   5   4   6   2 |     CGA   2   2   2   2   2   2
    CTG   9   9   9   9   8   7 |     CCG   2   2   2   2   2   3 |     CAG   6   6   6   6   6   7 |     CGG   0   0   0   0   0   1
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   4   5   5   4   5   6 | Thr ACT   2   1   1   3   3   4 | Asn AAT  14  14  14  13  12  11 | Ser AGT   4   4   4   3   5   6
    ATC   4   4   4   4   4   5 |     ACC  11  11  11   9  10   5 |     AAC  11  11  11  11  13  11 |     AGC   5   6   6   7   5   5
    ATA   6   6   6   6   6   6 |     ACA   3   3   3   3   3   3 | Lys AAA   4   4   4   4   2   2 | Arg AGA   1   0   0   0   0   1
Met ATG   2   2   2   2   2   1 |     ACG   0   0   0   1   1   0 |     AAG   3   3   3   4   3   3 |     AGG   3   3   3   3   2   5
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   3   3   3   3   2   5 | Ala GCT   4   4   4   4   4   4 | Asp GAT   2   3   3   1   1   2 | Gly GGT   2   2   2   2   2   2
    GTC   9   9   9   9  10   8 |     GCC   4   4   4   4   3   3 |     GAC   5   4   4   5   5   5 |     GGC   1   1   1   1   1   1
    GTA   7   7   7   6   6   6 |     GCA   4   4   4   4   4   2 | Glu GAA   8   8   8   9   9   9 |     GGA   5   5   5   5   5   7
    GTG   6   6   6   5   5   7 |     GCG   0   0   0   0   0   0 |     GAG   6   6   6   6   7   5 |     GGG   5   5   5   5   5   5
--------------------------------------------------------------------------------------------------------------------------------------

--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   0   0   0   0   0   0 | Ser TCT   0   0   0   0   0   0 | Tyr TAT   5   6   5   5   5   5 | Cys TGT   2   2   2   2   2   2
    TTC   4   4   4   4   4   4 |     TCC   5   6   6   5   5   5 |     TAC   5   5   5   4   4   4 |     TGC   0   0   0   0   0   0
Leu TTA   1   1   1   1   1   1 |     TCA   2   2   3   2   2   2 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
    TTG   0   0   0   0   0   0 |     TCG   1   1   1   1   1   1 |     TAG   0   0   0   0   0   0 | Trp TGG   3   3   3   3   3   3
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   2   2   2   2   2   2 | Pro CCT   2   2   2   3   3   3 | His CAT   1   0   0   0   0   0 | Arg CGT   0   0   0   0   0   0
    CTC   5   6   5   5   5   5 |     CCC   5   4   4   3   3   3 |     CAC   3   3   3   4   4   4 |     CGC   2   3   3   4   4   4
    CTA   3   3   3   3   3   3 |     CCA   7   7   5   7   7   7 | Gln CAA   2   3   3   2   2   2 |     CGA   2   2   2   2   2   2
    CTG   9   9   9   9   9   9 |     CCG   3   2   2   2   2   2 |     CAG   5   6   6   6   6   6 |     CGG   1   1   1   1   1   1
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   6   5   5   5   5   5 | Thr ACT   3   3   3   3   3   3 | Asn AAT  10   8   9   8   8   8 | Ser AGT   5   5   6   6   6   6
    ATC   3   3   4   5   5   5 |     ACC   7   8   8   8   8   8 |     AAC  12  10  10  11  11  11 |     AGC   5   6   5   6   6   6
    ATA   6   5   6   5   5   6 |     ACA   4   3   4   5   4   3 | Lys AAA   3   2   2   3   3   3 | Arg AGA   0   0   0   0   0   0
Met ATG   3   2   2   2   2   2 |     ACG   0   1   1   0   1   1 |     AAG   3   3   3   3   3   3 |     AGG   5   5   5   5   5   5
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   4   5   5   5   5   5 | Ala GCT   6   5   5   5   5   5 | Asp GAT   2   2   2   2   2   2 | Gly GGT   2   2   2   2   2   2
    GTC   8   8   8   7   7   7 |     GCC   2   3   3   3   3   3 |     GAC   6   6   6   6   6   6 |     GGC   1   2   2   1   1   1
    GTA   6   7   6   6   6   6 |     GCA   2   2   2   2   2   2 | Glu GAA   9   9   9   9   9   9 |     GGA   7   7   7   6   6   6
    GTG   7   7   7   7   7   7 |     GCG   0   0   0   0   0   0 |     GAG   5   5   5   5   5   5 |     GGG   5   5   5   6   6   6
--------------------------------------------------------------------------------------------------------------------------------------

----------------------------------------------------------------------------------------------------------------------
Phe TTT   0   0   0   1   1 | Ser TCT   0   2   2   1   1 | Tyr TAT   5   2   3   2   3 | Cys TGT   2   2   2   2   2
    TTC   4   2   2   2   4 |     TCC   6   2   4   4   4 |     TAC   5   7   7   8   5 |     TGC   0   0   0   0   0
Leu TTA   1   1   1   1   1 |     TCA   3   2   1   2   4 | *** TAA   0   0   0   0   0 | *** TGA   0   0   0   0   0
    TTG   0   0   0   0   1 |     TCG   1   0   0   0   0 |     TAG   0   0   0   0   0 | Trp TGG   3   3   3   3   3
----------------------------------------------------------------------------------------------------------------------
Leu CTT   2   4   6   4   3 | Pro CCT   2   2   2   2   2 | His CAT   0   0   1   1   0 | Arg CGT   0   0   0   0   0
    CTC   5   7   3   7   3 |     CCC   4   8   9   9   9 |     CAC   2   2   1   1   3 |     CGC   3   2   1   2   3
    CTA   3   2   3   2   2 |     CCA   5   5   7   3   2 | Gln CAA   2   1   2   2   2 |     CGA   2   3   3   3   1
    CTG   9   9   8  10   9 |     CCG   2   2   2   2   1 |     CAG   6   9   7   6   6 |     CGG   1   0   0   0   2
----------------------------------------------------------------------------------------------------------------------
Ile ATT   6   3   5   3   4 | Thr ACT   2   5   3   3   4 | Asn AAT  10   8   7   4   4 | Ser AGT   5   6   8   7   6
    ATC   4   3   4   2   4 |     ACC   8   9   8   9   9 |     AAC  12   9  10  12  12 |     AGC   6   7   8   8  11
    ATA   5   4   4   6   6 |     ACA   5   7   6   8   5 | Lys AAA   3   2   1   1   1 | Arg AGA   0   2   0   2   1
Met ATG   2   2   2   3   2 |     ACG   1   1   1   0   1 |     AAG   3   3   3   3   2 |     AGG   5   3   4   4   4
----------------------------------------------------------------------------------------------------------------------
Val GTT   4   4   5   3   5 | Ala GCT   5   3   5   3   4 | Asp GAT   2   3   2   3   2 | Gly GGT   2   2   0   2   1
    GTC   8   9   7   9   9 |     GCC   3   4   3   6   2 |     GAC   6   7   9   6   6 |     GGC   1   2   2   2   4
    GTA   6   3   3   3   3 |     GCA   2   3   3   2   3 | Glu GAA   9   5   7   7   7 |     GGA   6   4   6   5   4
    GTG   7  11  10   8   9 |     GCG   0   2   1   3   2 |     GAG   5   8   6   6   7 |     GGG   6   4   4   4   6
----------------------------------------------------------------------------------------------------------------------

Codon position x base (3x4) table for each sequence.

#1: human          
position  1:    T:0.11454    C:0.23348    A:0.33921    G:0.31278
position  2:    T:0.29075    C:0.21145    A:0.34361    G:0.15419
position  3:    T:0.21586    C:0.34361    A:0.23789    G:0.20264
Average         T:0.20705    C:0.26285    A:0.30690    G:0.22320

#2: chimpanzee     
position  1:    T:0.11454    C:0.23348    A:0.33921    G:0.31278
position  2:    T:0.29515    C:0.20705    A:0.34361    G:0.15419
position  3:    T:0.22026    C:0.34361    A:0.23348    G:0.20264
Average         T:0.20999    C:0.26138    A:0.30543    G:0.22320

#3: bonobo         
position  1:    T:0.11454    C:0.23348    A:0.33921    G:0.31278
position  2:    T:0.29515    C:0.20705    A:0.34361    G:0.15419
position  3:    T:0.22467    C:0.33480    A:0.23789    G:0.20264
Average         T:0.21145    C:0.25844    A:0.30690    G:0.22320

#4: gorilla        
position  1:    T:0.12335    C:0.23348    A:0.33921    G:0.30396
position  2:    T:0.28634    C:0.22026    A:0.33921    G:0.15419
position  3:    T:0.20264    C:0.35242    A:0.23789    G:0.20705
Average         T:0.20411    C:0.26872    A:0.30543    G:0.22173

#5: orangutan      
position  1:    T:0.11894    C:0.24229    A:0.33480    G:0.30396
position  2:    T:0.28634    C:0.22026    A:0.34361    G:0.14978
position  3:    T:0.21145    C:0.35242    A:0.23789    G:0.19824
Average         T:0.20558    C:0.27166    A:0.30543    G:0.21733

#6: colobus        
position  1:    T:0.11894    C:0.24229    A:0.32599    G:0.31278
position  2:    T:0.29956    C:0.19824    A:0.31278    G:0.18943
position  3:    T:0.24670    C:0.30837    A:0.23789    G:0.20705
Average         T:0.22173    C:0.24963    A:0.29222    G:0.23642

#7: AGM            
position  1:    T:0.12335    C:0.22907    A:0.33040    G:0.31718
position  2:    T:0.29515    C:0.21586    A:0.31278    G:0.17621
position  3:    T:0.22026    C:0.32159    A:0.23789    G:0.22026
Average         T:0.21292    C:0.25551    A:0.29369    G:0.23789

#8: baboon         
position  1:    T:0.13216    C:0.23348    A:0.30396    G:0.33040
position  2:    T:0.29515    C:0.21586    A:0.29956    G:0.18943
position  3:    T:0.20705    C:0.33921    A:0.23348    G:0.22026
Average         T:0.21145    C:0.26285    A:0.27900    G:0.24670

#9: sootyM         
position  1:    T:0.13216    C:0.22026    A:0.32159    G:0.32599
position  2:    T:0.29515    C:0.21586    A:0.29956    G:0.18943
position  3:    T:0.21145    C:0.33480    A:0.23348    G:0.22026
Average         T:0.21292    C:0.25698    A:0.28488    G:0.24523

#10: CEmac          
position  1:    T:0.11894    C:0.23348    A:0.33040    G:0.31718
position  2:    T:0.29075    C:0.21586    A:0.29956    G:0.19383
position  3:    T:0.21145    C:0.33480    A:0.23348    G:0.22026
Average         T:0.20705    C:0.26138    A:0.28781    G:0.24376

#11: rhesus         
position  1:    T:0.11894    C:0.23348    A:0.33040    G:0.31718
position  2:    T:0.29075    C:0.21586    A:0.29956    G:0.19383
position  3:    T:0.21145    C:0.33480    A:0.22907    G:0.22467
Average         T:0.20705    C:0.26138    A:0.28634    G:0.24523

#12: PTmac          
position  1:    T:0.11894    C:0.23348    A:0.33040    G:0.31718
position  2:    T:0.29515    C:0.21145    A:0.29956    G:0.19383
position  3:    T:0.21145    C:0.33480    A:0.22907    G:0.22467
Average         T:0.20852    C:0.25991    A:0.28634    G:0.24523

#13: drill          
position  1:    T:0.13216    C:0.21145    A:0.33921    G:0.31718
position  2:    T:0.29075    C:0.21586    A:0.30837    G:0.18502
position  3:    T:0.20705    C:0.33921    A:0.22907    G:0.22467
Average         T:0.20999    C:0.25551    A:0.29222    G:0.24229

#14: capuchin       
position  1:    T:0.10132    C:0.24670    A:0.32599    G:0.32599
position  2:    T:0.28194    C:0.25110    A:0.29075    G:0.17621
position  3:    T:0.20264    C:0.35242    A:0.19383    G:0.25110
Average         T:0.19530    C:0.28341    A:0.27019    G:0.25110

#15: squirrelM      
position  1:    T:0.11013    C:0.24229    A:0.32599    G:0.32159
position  2:    T:0.27753    C:0.25110    A:0.29075    G:0.18062
position  3:    T:0.22467    C:0.34361    A:0.20705    G:0.22467
Average         T:0.20411    C:0.27900    A:0.27460    G:0.24229

#16: nightM         
position  1:    T:0.11454    C:0.23789    A:0.33040    G:0.31718
position  2:    T:0.28194    C:0.25110    A:0.27313    G:0.19383
position  3:    T:0.18062    C:0.38326    A:0.20705    G:0.22907
Average         T:0.19236    C:0.29075    A:0.27019    G:0.24670

#17: marmoset       
position  1:    T:0.12775    C:0.21145    A:0.33480    G:0.32599
position  2:    T:0.29075    C:0.23348    A:0.26432    G:0.21145
position  3:    T:0.18502    C:0.38767    A:0.18502    G:0.24229
Average         T:0.20117    C:0.27753    A:0.26138    G:0.25991

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       2 | Ser S TCT       6 | Tyr Y TAT      76 | Cys C TGT      34
      TTC      62 |       TCC      75 |       TAC      89 |       TGC       0
Leu L TTA      17 |       TCA      37 | *** * TAA       0 | *** * TGA       0
      TTG       1 |       TCG      12 |       TAG       0 | Trp W TGG      51
------------------------------------------------------------------------------
Leu L CTT      48 | Pro P CCT      40 | His H CAT      14 | Arg R CGT       1
      CTC      86 |       CCC      95 |       CAC      45 |       CGC      43
      CTA      52 |       CCA      88 | Gln Q CAA      48 |       CGA      36
      CTG     150 |       CCG      35 |       CAG     106 |       CGG      10
------------------------------------------------------------------------------
Ile I ATT      81 | Thr T ACT      49 | Asn N AAT     162 | Ser S AGT      92
      ATC      67 |       ACC     147 |       AAC     188 |       AGC     108
      ATA      94 |       ACA      72 | Lys K AAA      44 | Arg R AGA       7
Met M ATG      35 |       ACG      10 |       AAG      51 |       AGG      69
------------------------------------------------------------------------------
Val V GTT      69 | Ala A GCT      75 | Asp D GAT      36 | Gly G GGT      31
      GTC     141 |       GCC      57 |       GAC      98 |       GGC      25
      GTA      94 |       GCA      47 | Glu E GAA     140 |       GGA      96
      GTG     122 |       GCG       8 |       GAG      98 |       GGG      87
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.11972    C:0.23244    A:0.33066    G:0.31718
position  2:    T:0.29049    C:0.22104    A:0.30967    G:0.17880
position  3:    T:0.21145    C:0.34361    A:0.22597    G:0.21897
Average         T:0.20722    C:0.26570    A:0.28876    G:0.23832

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
  0.00751412  0.01221044  0.00802979  0.00778117
  0.00571770  0.00929127  0.00611009  0.00592090
  0.00801015  0.01301649  0.00000000  0.00000000
  0.00462510  0.00751580  0.00000000  0.00478948
  0.01458910  0.02370729  0.01559032  0.01510759
  0.01110125  0.01803954  0.01186310  0.01149578
  0.01555217  0.02527227  0.01661947  0.01610488
  0.00897991  0.01459236  0.00959618  0.00929905
  0.02075328  0.03372409  0.02217753  0.02149084
  0.01579175  0.02566159  0.01687550  0.01635298
  0.02212326  0.03595030  0.02364152  0.02290950
  0.01277410  0.02075791  0.01365075  0.01322808
  0.01990754  0.03234975  0.02127374  0.02061504
  0.01514820  0.02461582  0.01618778  0.01568655
  0.02122168  0.03448524  0.02267807  0.02197589
  0.01225352  0.01991198  0.01309445  0.01268901


Model 1: NearlyNeutral (2 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), (((((11, 10), 12), (8, (9, 13))), 7), 6)), ((15, 14), (17, 16)));   MP score: 307
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 32  np: 35):  -2701.994001      +0.000000
  18..19   19..20   20..21   21..22   22..1    22..23   23..2    23..3    21..4    20..5    19..24   24..25   25..26   26..27   27..28   28..11   28..10   27..12   26..29   29..8    29..30   30..9    30..13   25..7    24..6    18..31   31..32   32..15   32..14   31..33   33..17   33..16 
 0.183719 0.061955 0.007814 0.017194 0.004474 0.008873 0.000004 0.008899 0.051669 0.057242 0.095642 0.049316 0.030986 0.027503 0.004514 0.000004 0.004515 0.000004 0.013630 0.018331 0.009123 0.000004 0.041199 0.038562 0.098911 0.186189 0.036221 0.113743 0.182753 0.026023 0.157044 0.136824 2.795622 0.414264 0.049520

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  1.672885

(((((1: 0.004474, (2: 0.000004, 3: 0.008899): 0.008873): 0.017194, 4: 0.051669): 0.007814, 5: 0.057242): 0.061955, (((((11: 0.000004, 10: 0.004515): 0.004514, 12: 0.000004): 0.027503, (8: 0.018331, (9: 0.000004, 13: 0.041199): 0.009123): 0.013630): 0.030986, 7: 0.038562): 0.049316, 6: 0.098911): 0.095642): 0.183719, ((15: 0.113743, 14: 0.182753): 0.036221, (17: 0.157044, 16: 0.136824): 0.026023): 0.186189);

(((((human: 0.004474, (chimpanzee: 0.000004, bonobo: 0.008899): 0.008873): 0.017194, gorilla: 0.051669): 0.007814, orangutan: 0.057242): 0.061955, (((((rhesus: 0.000004, CEmac: 0.004515): 0.004514, PTmac: 0.000004): 0.027503, (baboon: 0.018331, (sootyM: 0.000004, drill: 0.041199): 0.009123): 0.013630): 0.030986, AGM: 0.038562): 0.049316, colobus: 0.098911): 0.095642): 0.183719, ((squirrelM: 0.113743, capuchin: 0.182753): 0.036221, (marmoset: 0.157044, nightM: 0.136824): 0.026023): 0.186189);

Detailed output identifying parameters

kappa (ts/tv) =  2.79562


MLEs of dN/dS (w) for site classes (K=2)

p:   0.41426  0.58574
w:   0.04952  1.00000

dN & dS for each branch

 branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

  18..19      0.184    498.1    182.9   0.6063   0.0521   0.0860   26.0   15.7
  19..20      0.062    498.1    182.9   0.6063   0.0176   0.0290    8.8    5.3
  20..21      0.008    498.1    182.9   0.6063   0.0022   0.0037    1.1    0.7
  21..22      0.017    498.1    182.9   0.6063   0.0049   0.0080    2.4    1.5
  22..1       0.004    498.1    182.9   0.6063   0.0013   0.0021    0.6    0.4
  22..23      0.009    498.1    182.9   0.6063   0.0025   0.0042    1.3    0.8
  23..2       0.000    498.1    182.9   0.6063   0.0000   0.0000    0.0    0.0
  23..3       0.009    498.1    182.9   0.6063   0.0025   0.0042    1.3    0.8
  21..4       0.052    498.1    182.9   0.6063   0.0147   0.0242    7.3    4.4
  20..5       0.057    498.1    182.9   0.6063   0.0162   0.0268    8.1    4.9
  19..24      0.096    498.1    182.9   0.6063   0.0271   0.0448   13.5    8.2
  24..25      0.049    498.1    182.9   0.6063   0.0140   0.0231    7.0    4.2
  25..26      0.031    498.1    182.9   0.6063   0.0088   0.0145    4.4    2.7
  26..27      0.028    498.1    182.9   0.6063   0.0078   0.0129    3.9    2.4
  27..28      0.005    498.1    182.9   0.6063   0.0013   0.0021    0.6    0.4
  28..11      0.000    498.1    182.9   0.6063   0.0000   0.0000    0.0    0.0
  28..10      0.005    498.1    182.9   0.6063   0.0013   0.0021    0.6    0.4
  27..12      0.000    498.1    182.9   0.6063   0.0000   0.0000    0.0    0.0
  26..29      0.014    498.1    182.9   0.6063   0.0039   0.0064    1.9    1.2
  29..8       0.018    498.1    182.9   0.6063   0.0052   0.0086    2.6    1.6
  29..30      0.009    498.1    182.9   0.6063   0.0026   0.0043    1.3    0.8
  30..9       0.000    498.1    182.9   0.6063   0.0000   0.0000    0.0    0.0
  30..13      0.041    498.1    182.9   0.6063   0.0117   0.0193    5.8    3.5
  25..7       0.039    498.1    182.9   0.6063   0.0109   0.0181    5.5    3.3
  24..6       0.099    498.1    182.9   0.6063   0.0281   0.0463   14.0    8.5
  18..31      0.186    498.1    182.9   0.6063   0.0528   0.0872   26.3   15.9
  31..32      0.036    498.1    182.9   0.6063   0.0103   0.0170    5.1    3.1
  32..15      0.114    498.1    182.9   0.6063   0.0323   0.0533   16.1    9.7
  32..14      0.183    498.1    182.9   0.6063   0.0519   0.0856   25.8   15.6
  31..33      0.026    498.1    182.9   0.6063   0.0074   0.0122    3.7    2.2
  33..17      0.157    498.1    182.9   0.6063   0.0446   0.0735   22.2   13.4
  33..16      0.137    498.1    182.9   0.6063   0.0388   0.0641   19.3   11.7


Time used:  2:28


Model 2: PositiveSelection (3 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), (((((11, 10), 12), (8, (9, 13))), 7), 6)), ((15, 14), (17, 16)));   MP score: 307
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 32  np: 37):  -2686.334151      +0.000000
  18..19   19..20   20..21   21..22   22..1    22..23   23..2    23..3    21..4    20..5    19..24   24..25   25..26   26..27   27..28   28..11   28..10   27..12   26..29   29..8    29..30   30..9    30..13   25..7    24..6    18..31   31..32   32..15   32..14   31..33   33..17   33..16 
 0.231230 0.059954 0.008576 0.017504 0.004531 0.008924 0.000004 0.008976 0.052293 0.057464 0.103072 0.049322 0.031022 0.027911 0.004532 0.000004 0.004540 0.000004 0.013602 0.018518 0.009181 0.000004 0.041682 0.039375 0.101870 0.162340 0.031363 0.121345 0.194712 0.028309 0.163352 0.143198 3.036740 0.380548 0.497767 0.063063 3.668762

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  1.738715

(((((1: 0.004531, (2: 0.000004, 3: 0.008976): 0.008924): 0.017504, 4: 0.052293): 0.008576, 5: 0.057464): 0.059954, (((((11: 0.000004, 10: 0.004540): 0.004532, 12: 0.000004): 0.027911, (8: 0.018518, (9: 0.000004, 13: 0.041682): 0.009181): 0.013602): 0.031022, 7: 0.039375): 0.049322, 6: 0.101870): 0.103072): 0.231230, ((15: 0.121345, 14: 0.194712): 0.031363, (17: 0.163352, 16: 0.143198): 0.028309): 0.162340);

(((((human: 0.004531, (chimpanzee: 0.000004, bonobo: 0.008976): 0.008924): 0.017504, gorilla: 0.052293): 0.008576, orangutan: 0.057464): 0.059954, (((((rhesus: 0.000004, CEmac: 0.004540): 0.004532, PTmac: 0.000004): 0.027911, (baboon: 0.018518, (sootyM: 0.000004, drill: 0.041682): 0.009181): 0.013602): 0.031022, AGM: 0.039375): 0.049322, colobus: 0.101870): 0.103072): 0.231230, ((squirrelM: 0.121345, capuchin: 0.194712): 0.031363, (marmoset: 0.163352, nightM: 0.143198): 0.028309): 0.162340);

Detailed output identifying parameters

kappa (ts/tv) =  3.03674


MLEs of dN/dS (w) for site classes (K=3)

p:   0.38055  0.49777  0.12168
w:   0.06306  1.00000  3.66876

dN & dS for each branch

 branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

  18..19      0.231    496.2    184.8   0.9682   0.0764   0.0789   37.9   14.6
  19..20      0.060    496.2    184.8   0.9682   0.0198   0.0205    9.8    3.8
  20..21      0.009    496.2    184.8   0.9682   0.0028   0.0029    1.4    0.5
  21..22      0.018    496.2    184.8   0.9682   0.0058   0.0060    2.9    1.1
  22..1       0.005    496.2    184.8   0.9682   0.0015   0.0015    0.7    0.3
  22..23      0.009    496.2    184.8   0.9682   0.0029   0.0030    1.5    0.6
  23..2       0.000    496.2    184.8   0.9682   0.0000   0.0000    0.0    0.0
  23..3       0.009    496.2    184.8   0.9682   0.0030   0.0031    1.5    0.6
  21..4       0.052    496.2    184.8   0.9682   0.0173   0.0178    8.6    3.3
  20..5       0.057    496.2    184.8   0.9682   0.0190   0.0196    9.4    3.6
  19..24      0.103    496.2    184.8   0.9682   0.0341   0.0352   16.9    6.5
  24..25      0.049    496.2    184.8   0.9682   0.0163   0.0168    8.1    3.1
  25..26      0.031    496.2    184.8   0.9682   0.0102   0.0106    5.1    2.0
  26..27      0.028    496.2    184.8   0.9682   0.0092   0.0095    4.6    1.8
  27..28      0.005    496.2    184.8   0.9682   0.0015   0.0015    0.7    0.3
  28..11      0.000    496.2    184.8   0.9682   0.0000   0.0000    0.0    0.0
  28..10      0.005    496.2    184.8   0.9682   0.0015   0.0015    0.7    0.3
  27..12      0.000    496.2    184.8   0.9682   0.0000   0.0000    0.0    0.0
  26..29      0.014    496.2    184.8   0.9682   0.0045   0.0046    2.2    0.9
  29..8       0.019    496.2    184.8   0.9682   0.0061   0.0063    3.0    1.2
  29..30      0.009    496.2    184.8   0.9682   0.0030   0.0031    1.5    0.6
  30..9       0.000    496.2    184.8   0.9682   0.0000   0.0000    0.0    0.0
  30..13      0.042    496.2    184.8   0.9682   0.0138   0.0142    6.8    2.6
  25..7       0.039    496.2    184.8   0.9682   0.0130   0.0134    6.5    2.5
  24..6       0.102    496.2    184.8   0.9682   0.0337   0.0348   16.7    6.4
  18..31      0.162    496.2    184.8   0.9682   0.0536   0.0554   26.6   10.2
  31..32      0.031    496.2    184.8   0.9682   0.0104   0.0107    5.1    2.0
  32..15      0.121    496.2    184.8   0.9682   0.0401   0.0414   19.9    7.7
  32..14      0.195    496.2    184.8   0.9682   0.0643   0.0664   31.9   12.3
  31..33      0.028    496.2    184.8   0.9682   0.0094   0.0097    4.6    1.8
  33..17      0.163    496.2    184.8   0.9682   0.0540   0.0557   26.8   10.3
  33..16      0.143    496.2    184.8   0.9682   0.0473   0.0489   23.5    9.0


Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: human)

            Pr(w>1)     post mean +- SE for w

     2 T      0.680         2.816
     3 N      0.632         2.686
    22 H      0.508         2.356
    24 E      0.674         2.798
    29 Y      0.620         2.655
    50 K      0.999**       3.665
    51 N      0.776         3.072
    52 S      0.999**       3.666
    55 N      0.829         3.212
    67 I      0.676         2.805
    89 H      0.875         3.335
    92 K      0.732         2.953
    93 E      0.895         3.388
    96 V      0.863         3.303
    97 N      0.965*        3.576
   161 T      0.977*        3.608
   186 P      0.834         3.227
   203 Q      0.624         2.665


Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: human)

            Pr(w>1)     post mean +- SE for w

     2 T      0.735         2.714 +- 1.240
     3 N      0.697         2.600 +- 1.239
    22 H      0.602         2.352 +- 1.259
    24 E      0.730         2.704 +- 1.245
    29 Y      0.689         2.602 +- 1.278
    49 V      0.564         2.246 +- 1.241
    50 K      0.999**       3.517 +- 0.965
    51 N      0.811         2.945 +- 1.216
    52 S      0.999**       3.518 +- 0.965
    55 N      0.855         3.090 +- 1.194
    67 I      0.732         2.718 +- 1.258
    79 T      0.572         2.248 +- 1.209
    89 H      0.891         3.187 +- 1.142
    92 K      0.773         2.815 +- 1.213
    93 E      0.908         3.240 +- 1.123
    96 V      0.882         3.165 +- 1.160
    97 N      0.969*        3.434 +- 1.032
   155 P      0.521         2.123 +- 1.205
   161 T      0.980*        3.467 +- 1.012
   167 V      0.539         2.175 +- 1.222
   173 K      0.558         2.223 +- 1.224
   186 P      0.861         3.112 +- 1.194
   203 Q      0.693         2.614 +- 1.281
   204 A      0.595         2.323 +- 1.241



The grid (see ternary graph for p0-p1)

w0:   0.050  0.150  0.250  0.350  0.450  0.550  0.650  0.750  0.850  0.950
w2:   1.500  2.500  3.500  4.500  5.500  6.500  7.500  8.500  9.500 10.500


Posterior on the grid

w0:   0.383  0.374  0.193  0.045  0.005  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.302  0.478  0.146  0.051  0.015  0.004  0.001  0.000  0.000

Posterior for p0-p1 (see the ternary graph) (YWN2015, fig. 1)

 0.000
 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.002
 0.000 0.000 0.000 0.000 0.002 0.021 0.018
 0.000 0.000 0.000 0.000 0.000 0.005 0.100 0.104 0.006
 0.000 0.000 0.000 0.000 0.000 0.000 0.008 0.086 0.145 0.027 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.009 0.038 0.095 0.049 0.002 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.005 0.033 0.045 0.036 0.009 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.017 0.040 0.023 0.008 0.001 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.009 0.021 0.023 0.008 0.002 0.000 0.000 0.000

sum of density on p0-p1 =   1.000000

Time used:  7:18


Model 7: beta (10 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), (((((11, 10), 12), (8, (9, 13))), 7), 6)), ((15, 14), (17, 16)));   MP score: 307
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 32  np: 35):  -2702.213845      +0.000000
  18..19   19..20   20..21   21..22   22..1    22..23   23..2    23..3    21..4    20..5    19..24   24..25   25..26   26..27   27..28   28..11   28..10   27..12   26..29   29..8    29..30   30..9    30..13   25..7    24..6    18..31   31..32   32..15   32..14   31..33   33..17   33..16 
 0.207220 0.061664 0.007819 0.017109 0.004455 0.008834 0.000004 0.008863 0.051456 0.056960 0.095243 0.049181 0.030854 0.027394 0.004497 0.000004 0.004499 0.000004 0.013583 0.018264 0.009092 0.000004 0.041047 0.038433 0.098481 0.161041 0.036140 0.113132 0.181882 0.025914 0.156252 0.136136 2.804639 0.028670 0.016702

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  1.665463

(((((1: 0.004455, (2: 0.000004, 3: 0.008863): 0.008834): 0.017109, 4: 0.051456): 0.007819, 5: 0.056960): 0.061664, (((((11: 0.000004, 10: 0.004499): 0.004497, 12: 0.000004): 0.027394, (8: 0.018264, (9: 0.000004, 13: 0.041047): 0.009092): 0.013583): 0.030854, 7: 0.038433): 0.049181, 6: 0.098481): 0.095243): 0.207220, ((15: 0.113132, 14: 0.181882): 0.036140, (17: 0.156252, 16: 0.136136): 0.025914): 0.161041);

(((((human: 0.004455, (chimpanzee: 0.000004, bonobo: 0.008863): 0.008834): 0.017109, gorilla: 0.051456): 0.007819, orangutan: 0.056960): 0.061664, (((((rhesus: 0.000004, CEmac: 0.004499): 0.004497, PTmac: 0.000004): 0.027394, (baboon: 0.018264, (sootyM: 0.000004, drill: 0.041047): 0.009092): 0.013583): 0.030854, AGM: 0.038433): 0.049181, colobus: 0.098481): 0.095243): 0.207220, ((squirrelM: 0.113132, capuchin: 0.181882): 0.036140, (marmoset: 0.156252, nightM: 0.136136): 0.025914): 0.161041);

Detailed output identifying parameters

kappa (ts/tv) =  2.80464

Parameters in M7 (beta):
 p =   0.02867  q =   0.01670


MLEs of dN/dS (w) for site classes (K=10)

p:   0.10000  0.10000  0.10000  0.10000  0.10000  0.10000  0.10000  0.10000  0.10000  0.10000
w:   0.00000  0.00000  0.00000  0.14441  0.99976  1.00000  1.00000  1.00000  1.00000  1.00000

dN & dS for each branch

 branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

  18..19      0.207    498.0    183.0   0.6144   0.0591   0.0962   29.4   17.6
  19..20      0.062    498.0    183.0   0.6144   0.0176   0.0286    8.8    5.2
  20..21      0.008    498.0    183.0   0.6144   0.0022   0.0036    1.1    0.7
  21..22      0.017    498.0    183.0   0.6144   0.0049   0.0079    2.4    1.5
  22..1       0.004    498.0    183.0   0.6144   0.0013   0.0021    0.6    0.4
  22..23      0.009    498.0    183.0   0.6144   0.0025   0.0041    1.3    0.8
  23..2       0.000    498.0    183.0   0.6144   0.0000   0.0000    0.0    0.0
  23..3       0.009    498.0    183.0   0.6144   0.0025   0.0041    1.3    0.8
  21..4       0.051    498.0    183.0   0.6144   0.0147   0.0239    7.3    4.4
  20..5       0.057    498.0    183.0   0.6144   0.0162   0.0264    8.1    4.8
  19..24      0.095    498.0    183.0   0.6144   0.0272   0.0442   13.5    8.1
  24..25      0.049    498.0    183.0   0.6144   0.0140   0.0228    7.0    4.2
  25..26      0.031    498.0    183.0   0.6144   0.0088   0.0143    4.4    2.6
  26..27      0.027    498.0    183.0   0.6144   0.0078   0.0127    3.9    2.3
  27..28      0.004    498.0    183.0   0.6144   0.0013   0.0021    0.6    0.4
  28..11      0.000    498.0    183.0   0.6144   0.0000   0.0000    0.0    0.0
  28..10      0.004    498.0    183.0   0.6144   0.0013   0.0021    0.6    0.4
  27..12      0.000    498.0    183.0   0.6144   0.0000   0.0000    0.0    0.0
  26..29      0.014    498.0    183.0   0.6144   0.0039   0.0063    1.9    1.2
  29..8       0.018    498.0    183.0   0.6144   0.0052   0.0085    2.6    1.6
  29..30      0.009    498.0    183.0   0.6144   0.0026   0.0042    1.3    0.8
  30..9       0.000    498.0    183.0   0.6144   0.0000   0.0000    0.0    0.0
  30..13      0.041    498.0    183.0   0.6144   0.0117   0.0191    5.8    3.5
  25..7       0.038    498.0    183.0   0.6144   0.0110   0.0178    5.5    3.3
  24..6       0.098    498.0    183.0   0.6144   0.0281   0.0457   14.0    8.4
  18..31      0.161    498.0    183.0   0.6144   0.0459   0.0748   22.9   13.7
  31..32      0.036    498.0    183.0   0.6144   0.0103   0.0168    5.1    3.1
  32..15      0.113    498.0    183.0   0.6144   0.0323   0.0525   16.1    9.6
  32..14      0.182    498.0    183.0   0.6144   0.0519   0.0844   25.8   15.4
  31..33      0.026    498.0    183.0   0.6144   0.0074   0.0120    3.7    2.2
  33..17      0.156    498.0    183.0   0.6144   0.0446   0.0725   22.2   13.3
  33..16      0.136    498.0    183.0   0.6144   0.0388   0.0632   19.3   11.6


Time used: 21:16


Model 8: beta&w>1 (11 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), (((((11, 10), 12), (8, (9, 13))), 7), 6)), ((15, 14), (17, 16)));   MP score: 307
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 32  np: 37):  -2686.408440      +0.000000
  18..19   19..20   20..21   21..22   22..1    22..23   23..2    23..3    21..4    20..5    19..24   24..25   25..26   26..27   27..28   28..11   28..10   27..12   26..29   29..8    29..30   30..9    30..13   25..7    24..6    18..31   31..32   32..15   32..14   31..33   33..17   33..16 
 0.204302 0.059812 0.008630 0.017487 0.004529 0.008914 0.000004 0.008968 0.052252 0.057372 0.103178 0.049364 0.031007 0.027900 0.004529 0.000004 0.004537 0.000004 0.013597 0.018510 0.009176 0.000004 0.041670 0.039364 0.101808 0.189286 0.031058 0.121344 0.194644 0.028449 0.163257 0.143130 3.040520 0.887062 0.033356 0.019550 3.831067

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  1.738089

(((((1: 0.004529, (2: 0.000004, 3: 0.008968): 0.008914): 0.017487, 4: 0.052252): 0.008630, 5: 0.057372): 0.059812, (((((11: 0.000004, 10: 0.004537): 0.004529, 12: 0.000004): 0.027900, (8: 0.018510, (9: 0.000004, 13: 0.041670): 0.009176): 0.013597): 0.031007, 7: 0.039364): 0.049364, 6: 0.101808): 0.103178): 0.204302, ((15: 0.121344, 14: 0.194644): 0.031058, (17: 0.163257, 16: 0.143130): 0.028449): 0.189286);

(((((human: 0.004529, (chimpanzee: 0.000004, bonobo: 0.008968): 0.008914): 0.017487, gorilla: 0.052252): 0.008630, orangutan: 0.057372): 0.059812, (((((rhesus: 0.000004, CEmac: 0.004537): 0.004529, PTmac: 0.000004): 0.027900, (baboon: 0.018510, (sootyM: 0.000004, drill: 0.041670): 0.009176): 0.013597): 0.031007, AGM: 0.039364): 0.049364, colobus: 0.101808): 0.103178): 0.204302, ((squirrelM: 0.121344, capuchin: 0.194644): 0.031058, (marmoset: 0.163257, nightM: 0.143130): 0.028449): 0.189286);

Detailed output identifying parameters

kappa (ts/tv) =  3.04052

Parameters in M8 (beta&w>1):
  p0 =   0.88706  p =   0.03336 q =   0.01955
 (p1 =   0.11294) w =   3.83107


MLEs of dN/dS (w) for site classes (K=11)

p:   0.08871  0.08871  0.08871  0.08871  0.08871  0.08871  0.08871  0.08871  0.08871  0.08871  0.11294
w:   0.00000  0.00000  0.00001  0.16127  0.99912  1.00000  1.00000  1.00000  1.00000  1.00000  3.83107

dN & dS for each branch

 branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

  18..19      0.204    496.2    184.8   0.9791   0.0677   0.0692   33.6   12.8
  19..20      0.060    496.2    184.8   0.9791   0.0198   0.0202    9.8    3.7
  20..21      0.009    496.2    184.8   0.9791   0.0029   0.0029    1.4    0.5
  21..22      0.017    496.2    184.8   0.9791   0.0058   0.0059    2.9    1.1
  22..1       0.005    496.2    184.8   0.9791   0.0015   0.0015    0.7    0.3
  22..23      0.009    496.2    184.8   0.9791   0.0030   0.0030    1.5    0.6
  23..2       0.000    496.2    184.8   0.9791   0.0000   0.0000    0.0    0.0
  23..3       0.009    496.2    184.8   0.9791   0.0030   0.0030    1.5    0.6
  21..4       0.052    496.2    184.8   0.9791   0.0173   0.0177    8.6    3.3
  20..5       0.057    496.2    184.8   0.9791   0.0190   0.0194    9.4    3.6
  19..24      0.103    496.2    184.8   0.9791   0.0342   0.0349   17.0    6.5
  24..25      0.049    496.2    184.8   0.9791   0.0164   0.0167    8.1    3.1
  25..26      0.031    496.2    184.8   0.9791   0.0103   0.0105    5.1    1.9
  26..27      0.028    496.2    184.8   0.9791   0.0092   0.0094    4.6    1.7
  27..28      0.005    496.2    184.8   0.9791   0.0015   0.0015    0.7    0.3
  28..11      0.000    496.2    184.8   0.9791   0.0000   0.0000    0.0    0.0
  28..10      0.005    496.2    184.8   0.9791   0.0015   0.0015    0.7    0.3
  27..12      0.000    496.2    184.8   0.9791   0.0000   0.0000    0.0    0.0
  26..29      0.014    496.2    184.8   0.9791   0.0045   0.0046    2.2    0.9
  29..8       0.019    496.2    184.8   0.9791   0.0061   0.0063    3.0    1.2
  29..30      0.009    496.2    184.8   0.9791   0.0030   0.0031    1.5    0.6
  30..9       0.000    496.2    184.8   0.9791   0.0000   0.0000    0.0    0.0
  30..13      0.042    496.2    184.8   0.9791   0.0138   0.0141    6.9    2.6
  25..7       0.039    496.2    184.8   0.9791   0.0130   0.0133    6.5    2.5
  24..6       0.102    496.2    184.8   0.9791   0.0337   0.0345   16.7    6.4
  18..31      0.189    496.2    184.8   0.9791   0.0627   0.0641   31.1   11.8
  31..32      0.031    496.2    184.8   0.9791   0.0103   0.0105    5.1    1.9
  32..15      0.121    496.2    184.8   0.9791   0.0402   0.0411   20.0    7.6
  32..14      0.195    496.2    184.8   0.9791   0.0645   0.0659   32.0   12.2
  31..33      0.028    496.2    184.8   0.9791   0.0094   0.0096    4.7    1.8
  33..17      0.163    496.2    184.8   0.9791   0.0541   0.0553   26.8   10.2
  33..16      0.143    496.2    184.8   0.9791   0.0474   0.0484   23.5    9.0


Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: human)

            Pr(w>1)     post mean +- SE for w

     2 T      0.654         2.852
     3 N      0.601         2.702
    24 E      0.648         2.833
    29 Y      0.593         2.679
    50 K      0.999**       3.828
    51 N      0.759         3.149
    52 S      0.999**       3.829
    55 N      0.817         3.314
    67 I      0.652         2.845
    89 H      0.866         3.453
    92 K      0.708         3.004
    93 E      0.888         3.514
    96 V      0.854         3.417
    97 N      0.964*        3.730
   161 T      0.977*        3.766
   186 P      0.824         3.332
   203 Q      0.597         2.691


Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: human)

            Pr(w>1)     post mean +- SE for w

     1 Q      0.557         1.862 +- 1.085
     2 T      0.905         2.682 +- 0.784
     3 N      0.889         2.643 +- 0.812
     6 V      0.648         2.072 +- 1.037
    22 H      0.808         2.454 +- 0.938
    24 E      0.902         2.675 +- 0.791
    26 Q      0.565         1.881 +- 1.089
    28 L      0.624         2.020 +- 1.083
    29 Y      0.860         2.580 +- 0.871
    43 Y      0.618         2.005 +- 1.083
    49 V      0.781         2.390 +- 0.965
    50 K      1.000**       2.901 +- 0.543
    51 N      0.936         2.756 +- 0.722
    52 S      1.000**       2.901 +- 0.543
    53 Q      0.566         1.884 +- 1.086
    54 E      0.722         2.248 +- 1.007
    55 N      0.950         2.789 +- 0.690
    57 P      0.619         2.008 +- 1.084
    63 G      0.510         1.752 +- 1.078
    67 I      0.893         2.655 +- 0.813
    71 G      0.548         1.840 +- 1.085
    79 T      0.818         2.471 +- 0.908
    83 A      0.516         1.765 +- 1.080
    89 H      0.969*        2.832 +- 0.638
    92 K      0.933         2.745 +- 0.723
    93 E      0.973*        2.843 +- 0.625
    96 V      0.962*        2.817 +- 0.657
    97 N      0.991**       2.883 +- 0.570
   101 T      0.672         2.128 +- 1.028
   102 R      0.572         1.894 +- 1.041
   107 F      0.701         2.198 +- 1.034
   108 S      0.617         2.003 +- 1.084
   109 E      0.644         2.066 +- 1.067
   130 V      0.506         1.742 +- 1.077
   152 L      0.614         1.996 +- 1.084
   155 P      0.753         2.322 +- 0.985
   161 T      0.994**       2.889 +- 0.562
   167 V      0.765         2.351 +- 0.977
   173 K      0.784         2.396 +- 0.958
   176 I      0.723         2.249 +- 1.006
   186 P      0.951*        2.792 +- 0.688
   187 V      0.589         1.936 +- 1.086
   203 Q      0.861         2.582 +- 0.871
   204 A      0.815         2.469 +- 0.923
   223 G      0.548         1.840 +- 1.085
   224 M      0.608         1.977 +- 1.041



The grid 

p0:   0.050  0.150  0.250  0.350  0.450  0.550  0.650  0.750  0.850  0.950
p :   0.100  0.300  0.500  0.700  0.900  1.100  1.300  1.500  1.700  1.900
q :   0.100  0.300  0.500  0.700  0.900  1.100  1.300  1.500  1.700  1.900
ws:   1.500  2.500  3.500  4.500  5.500  6.500  7.500  8.500  9.500 10.500


Posterior on the grid

p0:   0.000  0.000  0.000  0.000  0.000  0.001  0.155  0.504  0.337  0.002
p :   0.074  0.115  0.169  0.190  0.169  0.123  0.077  0.044  0.025  0.014
q :   0.073  0.076  0.089  0.094  0.101  0.106  0.111  0.115  0.117  0.119
ws:   0.000  0.622  0.356  0.021  0.001  0.000  0.000  0.000  0.000  0.000

Time used: 43:11
