7 390 Hsa_Human_ AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA Cgu/Can_co AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG Ssc_squirr AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA Cja_marmos AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA Printing out site pattern counts 7 243 P Hsa_Human_ AAA AAA AAC AAC AAG AAT AAT AAT AAT ACA ACC ACT AGA AGA AGA AGA AGA AGA AGC AGG AGG AGT AGT ATA ATC ATC ATG ATG ATT CAA CAA CAG CAT CCA CGA CGC CGT CGT CGT CTA CTG GAA GAC GAG GAT GAT GAT GAT GCA GCC GCT GCT GCT GCT GGA GGC GGG GGT GGT GTA GTC GTC GTC GTG GTG GTT GTT TAC TAC TAC TAT TAT TCC TGC TGG TGT TTA TTG TTG TTT TTT Hla_gibbon ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ..C ... ... ... ... ... ... ... ... C.. ... ... ..A ... A.. ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... Cgu/Can_co ... ... ... ... ... ..G ... ... ... ... ... ... .A. .A. ... ... C.. GA. ... .A. ... .A. ... ... ... G.. C.. G.. ... ... G.. ... ... ... GAC ... A.. A.. .AC ... ... ... ..T ... A.. A.. ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... A.. ... ..A ... ... ... ... ... ..T ... ... ... ... ... ... A.. ... ... ... ... Pne_langur ... ... ... ... ... ... ... ... G.. ... ... ... .A. ... .A. ... C.. GA. ... .A. ... ... ... ... ... G.. C.. G.. G.. ... A.. ... ... ... GA. ... A.. A.. .AC ... ... ... ... ... A.C A.. ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ..T ..C ... ... ... ... ... A.. ... ... ... ... Mmu_rhesus ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... CA. ... ... ... .A. ... ... ... ... C.. G.. ... ... ... ... ... ... .A. .A. A.. A.. .AC ... ... ... ... ... ... A.. ... ... ... ... C.. ... A.. ... ... ... ... AA. ... ... ... A.. ... ... ... ... ... ... ... ..T ... ... ... ... ... ... A.. ... ... ... ... Ssc_squirr ... .G. ... G.. ... GC. ... ... ... ... ... ... ..G .A. ... ... ... CA. ... ... ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ..T .A. ... A.. .A. ... ... ... ... ... ... A.. C.A ... ... ... C.. A.. ..C ... ... ... ... .AC ... ..G ... ... ... ..A ... ... ... ... ..T ..T ... ... ... ... ... ... A.. C.T ... ..C ... Cja_marmos ... .G. ... G.. ... GC. ..C ... ... ... ... ... ..G .A. ... ... ..G CA. ... ... ... .A. ... ... ... ... C.. ... ... ... ... ... ... ... ..T .A. ..C A.. .A. ... ... ... ... ... ... A.. ..A ... ... ... C.. A.. ..C ... ... ... ... .A. ... ..G ... ... ... ..A ... ... ... ... ..T ..T ... ... ... ... ... ... A.. ..T ... ... ... 2 1 4 1 2 1 1 2 1 2 1 2 1 1 1 1 1 1 3 1 2 1 1 1 2 1 1 1 1 3 1 2 1 2 1 1 1 1 1 1 2 1 1 2 1 1 1 4 5 3 1 1 1 3 5 3 1 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 5 7 1 1 3 1 1 CODONML (in paml version 4.10.0, September 2020) lysozymeSmall.phy Model: several dN/dS ratios for branches, Codon frequency model: F3x4 ns = 7 ls = 130 Codon usage in sequences -------------------------------------------------------------------------------------------------------------------------------------- Phe TTT 2 2 2 2 2 1 | Ser TCT 0 0 0 0 0 0 | Tyr TAT 2 3 3 2 3 4 | Cys TGT 7 7 7 7 7 7 TTC 0 0 0 0 0 1 | TCC 1 1 1 1 1 1 | TAC 4 3 3 4 3 2 | TGC 1 1 1 1 1 1 Leu TTA 1 1 0 0 0 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 4 4 4 4 4 3 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 5 5 5 5 5 5 -------------------------------------------------------------------------------------------------------------------------------------- Leu CTT 0 0 0 0 0 1 | Pro CCT 0 1 1 1 1 1 | His CAT 1 1 1 1 1 2 | Arg CGT 3 2 0 0 0 2 CTC 0 1 0 0 0 0 | CCC 0 0 0 0 0 0 | CAC 0 0 1 1 2 1 | CGC 1 2 1 1 0 0 CTA 1 1 1 1 1 1 | CCA 2 2 2 2 2 2 | Gln CAA 4 4 3 3 6 6 | CGA 1 1 1 1 0 0 CTG 2 2 3 3 3 2 | CCG 0 0 0 0 0 0 | CAG 2 2 2 2 2 2 | CGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------------------------------- Ile ATT 1 2 1 0 1 1 | Thr ACT 2 2 2 2 3 3 | Asn AAT 5 6 7 5 8 6 | Ser AGT 2 1 3 4 3 2 ATC 3 3 3 3 4 3 | ACC 1 1 1 1 1 1 | AAC 5 5 5 6 5 4 | AGC 3 3 3 3 3 3 ATA 1 1 2 2 2 2 | ACA 2 2 2 2 2 2 | Lys AAA 3 3 5 6 3 3 | Arg AGA 6 6 2 2 5 4 Met ATG 2 2 0 0 0 2 | ACG 0 0 0 0 0 0 | AAG 2 2 4 3 2 2 | AGG 3 3 2 2 3 4 -------------------------------------------------------------------------------------------------------------------------------------- Val GTT 3 2 3 4 3 3 | Ala GCT 6 4 5 5 4 4 | Asp GAT 7 7 6 6 6 5 | Gly GGT 2 2 2 2 1 1 GTC 3 2 3 3 2 3 | GCC 3 4 3 3 3 4 | GAC 1 1 1 1 1 3 | GGC 3 3 3 3 3 3 GTA 1 2 2 1 1 1 | GCA 5 5 5 5 5 5 | Glu GAA 1 1 3 3 1 1 | GGA 5 5 5 5 5 5 GTG 2 1 2 3 3 2 | GCG 0 0 0 0 0 0 | GAG 2 2 2 2 2 2 | GGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------------------------------- ------------------------------------------------------ Phe TTT 3 | Ser TCT 0 | Tyr TAT 4 | Cys TGT 7 TTC 0 | TCC 1 | TAC 2 | TGC 1 Leu TTA 0 | TCA 0 | *** TAA 0 | *** TGA 0 TTG 3 | TCG 0 | TAG 0 | Trp TGG 5 ------------------------------------------------------ Leu CTT 0 | Pro CCT 1 | His CAT 2 | Arg CGT 1 CTC 0 | CCC 0 | CAC 1 | CGC 1 CTA 1 | CCA 2 | Gln CAA 5 | CGA 0 CTG 3 | CCG 0 | CAG 2 | CGG 0 ------------------------------------------------------ Ile ATT 1 | Thr ACT 3 | Asn AAT 5 | Ser AGT 2 ATC 3 | ACC 1 | AAC 5 | AGC 3 ATA 2 | ACA 2 | Lys AAA 3 | Arg AGA 3 Met ATG 1 | ACG 0 | AAG 2 | AGG 5 ------------------------------------------------------ Val GTT 3 | Ala GCT 4 | Asp GAT 6 | Gly GGT 1 GTC 3 | GCC 4 | GAC 2 | GGC 3 GTA 1 | GCA 5 | Glu GAA 2 | GGA 5 GTG 2 | GCG 0 | GAG 2 | GGG 1 ------------------------------------------------------ Codon position x base (3x4) table for each sequence. #1: Hsa_Human_ position 1: T:0.20769 C:0.13077 A:0.31538 G:0.34615 position 2: T:0.20000 C:0.16923 A:0.30000 G:0.33077 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 Average T:0.24615 C:0.17436 A:0.28974 G:0.28974 #2: Hla_gibbon position 1: T:0.20769 C:0.14615 A:0.32308 G:0.32308 position 2: T:0.20000 C:0.16923 A:0.30769 G:0.32308 position 3: T:0.32308 C:0.23077 A:0.26154 G:0.18462 Average T:0.24359 C:0.18205 A:0.29744 G:0.27692 #3: Cgu/Can_co position 1: T:0.20000 C:0.12308 A:0.32308 G:0.35385 position 2: T:0.20000 C:0.16923 A:0.35385 G:0.27692 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 Average T:0.24359 C:0.17179 A:0.31026 G:0.27436 #4: Pne_langur position 1: T:0.20000 C:0.12308 A:0.31538 G:0.36154 position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462 position 3: T:0.31538 C:0.23846 A:0.25385 G:0.19231 Average T:0.23846 C:0.17692 A:0.30513 G:0.27949 #5: Mmu_rhesus position 1: T:0.20000 C:0.13846 A:0.34615 G:0.31538 position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231 Average T:0.24359 C:0.17692 A:0.31538 G:0.26410 #6: Ssc_squirr position 1: T:0.19231 C:0.15385 A:0.32308 G:0.33077 position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231 position 3: T:0.33077 C:0.23077 A:0.24615 G:0.19231 Average T:0.24103 C:0.18718 A:0.30000 G:0.27179 #7: Cja_marmos position 1: T:0.20000 C:0.14615 A:0.31538 G:0.33846 position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231 position 3: T:0.33077 C:0.23077 A:0.23846 G:0.20000 Average T:0.24359 C:0.18462 A:0.29487 G:0.27692 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 14 | Ser S TCT 0 | Tyr Y TAT 21 | Cys C TGT 49 TTC 1 | TCC 7 | TAC 21 | TGC 7 Leu L TTA 2 | TCA 0 | *** * TAA 0 | *** * TGA 0 TTG 26 | TCG 0 | TAG 0 | Trp W TGG 35 ------------------------------------------------------------------------------ Leu L CTT 1 | Pro P CCT 6 | His H CAT 9 | Arg R CGT 8 CTC 1 | CCC 0 | CAC 6 | CGC 6 CTA 7 | CCA 14 | Gln Q CAA 31 | CGA 4 CTG 18 | CCG 0 | CAG 14 | CGG 0 ------------------------------------------------------------------------------ Ile I ATT 7 | Thr T ACT 17 | Asn N AAT 42 | Ser S AGT 17 ATC 22 | ACC 7 | AAC 35 | AGC 21 ATA 12 | ACA 14 | Lys K AAA 26 | Arg R AGA 28 Met M ATG 7 | ACG 0 | AAG 17 | AGG 22 ------------------------------------------------------------------------------ Val V GTT 21 | Ala A GCT 32 | Asp D GAT 43 | Gly G GGT 11 GTC 19 | GCC 24 | GAC 10 | GGC 21 GTA 9 | GCA 35 | Glu E GAA 12 | GGA 35 GTG 15 | GCG 0 | GAG 14 | GGG 7 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.20110 C:0.13736 A:0.32308 G:0.33846 position 2: T:0.20000 C:0.17143 A:0.33077 G:0.29780 position 3: T:0.32747 C:0.22857 A:0.25165 G:0.19231 Average T:0.24286 C:0.17912 A:0.30183 G:0.27619 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): 0.01378574 0.00962226 0.01059374 0.00809565 0.01181635 0.00824765 0.00908035 0.00693913 0.02279949 0.01591374 0.00000000 0.00000000 0.02052711 0.01432765 0.00000000 0.01205451 0.00941649 0.00657258 0.00723616 0.00552982 0.00807127 0.00563364 0.00620242 0.00473984 0.01557342 0.01087004 0.01196749 0.00914546 0.01402125 0.00978665 0.01077472 0.00823396 0.02214758 0.01545871 0.01701945 0.01300613 0.01898364 0.01325032 0.01458810 0.01114811 0.03662868 0.02556633 0.02814755 0.02151013 0.03297798 0.02301819 0.02534214 0.01936627 0.02320222 0.01619484 0.01782990 0.01362547 0.01988762 0.01388129 0.01528277 0.01167897 0.03837291 0.02678377 0.02948791 0.02253443 0.03454836 0.02411429 0.02654891 0.02028847 TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 lnL(ntime: 11 np: 14): -904.636553 +0.000000 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7 0.070001 0.025569 0.038928 0.043879 0.079045 0.043878 0.052150 0.019487 0.121307 0.041033 0.023778 4.561199 0.685810 3.505718 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 0.559055 ((1: 0.025569, 2: 0.038928): 0.070001, ((3: 0.043878, 4: 0.052150): 0.079045, 5: 0.019487): 0.043879, (6: 0.041033, 7: 0.023778): 0.121307); ((Hsa_Human_: 0.025569, Hla_gibbon: 0.038928): 0.070001, ((Cgu/Can_co: 0.043878, Pne_langur: 0.052150): 0.079045, Mmu_rhesus: 0.019487): 0.043879, (Ssc_squirr: 0.041033, Cja_marmos: 0.023778): 0.121307); Detailed output identifying parameters kappa (ts/tv) = 4.56120 w (dN/dS) for branches: 0.68581 3.50572 dN & dS for each branch branch t N S dN/dS dN dS N*dN S*dS 8..9 0.070 282.2 107.8 0.6858 0.0207 0.0302 5.8 3.3 9..1 0.026 282.2 107.8 0.6858 0.0076 0.0110 2.1 1.2 9..2 0.039 282.2 107.8 0.6858 0.0115 0.0168 3.2 1.8 8..10 0.044 282.2 107.8 0.6858 0.0130 0.0189 3.7 2.0 10..11 0.079 282.2 107.8 3.5057 0.0328 0.0094 9.3 1.0 11..3 0.044 282.2 107.8 0.6858 0.0130 0.0189 3.7 2.0 11..4 0.052 282.2 107.8 0.6858 0.0154 0.0225 4.4 2.4 10..5 0.019 282.2 107.8 0.6858 0.0058 0.0084 1.6 0.9 8..12 0.121 282.2 107.8 0.6858 0.0359 0.0523 10.1 5.6 12..6 0.041 282.2 107.8 0.6858 0.0121 0.0177 3.4 1.9 12..7 0.024 282.2 107.8 0.6858 0.0070 0.0103 2.0 1.1 tree length for dN: 0.1749 tree length for dS: 0.2164 dS tree: ((Hsa_Human_: 0.011030, Hla_gibbon: 0.016794): 0.030198, ((Cgu/Can_co: 0.018929, Pne_langur: 0.022497): 0.009367, Mmu_rhesus: 0.008406): 0.018929, (Ssc_squirr: 0.017701, Cja_marmos: 0.010258): 0.052331); dN tree: ((Hsa_Human_: 0.007565, Hla_gibbon: 0.011517): 0.020710, ((Cgu/Can_co: 0.012981, Pne_langur: 0.015429): 0.032838, Mmu_rhesus: 0.005765): 0.012982, (Ssc_squirr: 0.012140, Cja_marmos: 0.007035): 0.035889); w ratios as labels for TreeView: ((Hsa_Human_ #0.68581 , Hla_gibbon #0.68581 ) #0.68581 , ((Cgu/Can_co #0.68581 , Pne_langur #0.68581 ) #3.50572 , Mmu_rhesus #0.68581 ) #0.68581 , (Ssc_squirr #0.68581 , Cja_marmos #0.68581 ) #0.68581 ); Time used: 0:02