CODONML (in paml version 4.10.0, September 2020) bglobin.phy Model: One dN/dS ratio, omega = 1.000 fixed Codon frequency model: F3x4 Site-class models: beta&w>1 (11 categories) ns = 17 ls = 144 Codon usage in sequences -------------------------------------------------------------------------------------------------------------------------------------- Phe TTT 5 5 5 2 3 7 | Ser TCT 1 0 2 3 3 0 | Tyr TAT 2 1 1 1 1 1 | Cys TGT 2 2 2 1 1 1 TTC 3 3 3 6 5 3 | TCC 2 2 2 3 3 3 | TAC 1 2 2 2 2 1 | TGC 0 0 0 0 0 0 Leu TTA 0 0 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 0 3 0 0 0 1 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 2 2 2 2 2 2 -------------------------------------------------------------------------------------------------------------------------------------- Leu CTT 0 0 0 0 0 0 | Pro CCT 5 2 4 3 3 2 | His CAT 2 2 1 3 3 4 | Arg CGT 0 0 0 0 0 0 CTC 3 2 2 2 2 3 | CCC 0 0 0 0 0 1 | CAC 6 6 7 5 5 2 | CGC 0 0 0 0 0 1 CTA 0 0 0 0 0 2 | CCA 2 1 2 1 1 0 | Gln CAA 0 0 0 0 0 0 | CGA 0 0 0 0 0 0 CTG 15 12 16 16 16 11 | CCG 0 1 0 0 0 1 | CAG 3 4 4 4 4 3 | CGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------------------------------- Ile ATT 0 0 0 1 1 0 | Thr ACT 3 4 2 3 2 3 | Asn AAT 1 3 3 2 4 3 | Ser AGT 2 2 2 3 4 2 ATC 0 0 0 0 0 0 | ACC 3 3 3 3 2 3 | AAC 5 2 4 4 4 4 | AGC 0 1 1 0 0 0 ATA 0 0 0 0 0 0 | ACA 1 0 0 0 0 0 | Lys AAA 3 3 2 3 3 1 | Arg AGA 0 0 0 0 0 1 Met ATG 1 2 1 1 1 2 | ACG 0 0 0 0 0 0 | AAG 8 9 10 9 9 12 | AGG 3 3 3 3 3 2 -------------------------------------------------------------------------------------------------------------------------------------- Val GTT 3 3 5 4 4 4 | Ala GCT 6 9 7 8 7 8 | Asp GAT 5 2 2 1 1 6 | Gly GGT 4 3 3 5 4 3 GTC 2 4 2 2 2 2 | GCC 9 10 7 5 6 7 | GAC 2 6 5 3 3 3 | GGC 8 7 8 7 6 7 GTA 0 1 0 0 0 0 | GCA 0 0 0 0 1 0 | Glu GAA 2 3 2 4 4 2 | GGA 0 0 0 0 0 0 GTG 12 9 11 11 11 12 | GCG 0 0 0 1 1 1 | GAG 6 4 5 6 6 6 | GGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------------- Phe TTT 5 3 6 3 4 4 | Ser TCT 0 1 2 2 4 2 | Tyr TAT 1 0 1 0 0 0 | Cys TGT 1 1 2 2 1 1 TTC 4 5 3 4 3 4 | TCC 2 3 4 1 1 2 | TAC 1 2 1 3 3 2 | TGC 0 0 0 0 1 0 Leu TTA 0 0 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 1 0 1 2 0 1 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 2 2 2 2 2 2 -------------------------------------------------------------------------------------------------------------------------------------- Leu CTT 0 1 0 0 0 1 | Pro CCT 2 1 1 4 3 2 | His CAT 3 2 2 3 2 2 | Arg CGT 0 0 0 0 0 0 CTC 3 5 4 3 4 2 | CCC 1 2 3 1 2 2 | CAC 6 5 4 6 5 8 | CGC 1 2 1 0 0 0 CTA 1 0 0 1 2 0 | CCA 0 0 1 0 0 1 | Gln CAA 0 0 0 0 0 0 | CGA 0 0 0 0 0 0 CTG 12 13 13 11 11 15 | CCG 1 1 0 0 0 0 | CAG 4 5 5 3 3 3 | CGG 0 0 0 0 1 0 -------------------------------------------------------------------------------------------------------------------------------------- Ile ATT 0 0 1 2 1 1 | Thr ACT 2 1 1 1 3 3 | Asn AAT 3 5 5 3 2 3 | Ser AGT 2 1 2 2 1 2 ATC 0 0 0 1 2 4 | ACC 3 1 3 3 3 1 | AAC 5 4 3 5 5 4 | AGC 0 1 1 1 2 1 ATA 0 1 0 1 1 0 | ACA 0 0 0 0 0 0 | Lys AAA 2 2 2 1 2 1 | Arg AGA 0 0 0 0 0 0 Met ATG 2 1 2 2 1 2 | ACG 0 0 1 0 0 0 | AAG 10 9 12 11 10 11 | AGG 3 3 2 3 2 2 -------------------------------------------------------------------------------------------------------------------------------------- Val GTT 5 5 2 3 2 3 | Ala GCT 9 7 3 8 7 6 | Asp GAT 5 2 3 6 5 4 | Gly GGT 2 3 4 2 3 1 GTC 2 3 3 1 2 3 | GCC 6 7 8 8 8 8 | GAC 4 6 4 3 3 5 | GGC 8 9 7 8 7 8 GTA 0 0 1 0 0 0 | GCA 0 0 0 1 2 2 | Glu GAA 2 1 3 2 1 1 | GGA 0 0 0 2 2 2 GTG 11 10 9 9 9 8 | GCG 0 0 1 0 1 0 | GAG 6 7 4 3 5 4 | GGG 1 1 1 1 0 0 -------------------------------------------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------------------------- Phe TTT 5 0 3 4 1 | Ser TCT 4 0 0 2 3 | Tyr TAT 1 0 0 1 1 | Cys TGT 2 1 2 0 0 TTC 2 8 5 3 4 | TCC 2 4 5 2 3 | TAC 2 2 2 2 2 | TGC 2 2 1 0 0 Leu TTA 0 0 0 0 1 | TCA 1 0 0 2 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0 TTG 4 0 0 2 0 | TCG 0 0 0 0 0 | TAG 0 0 0 0 0 | Trp TGG 3 4 4 4 4 ---------------------------------------------------------------------------------------------------------------------- Leu CTT 1 1 1 2 6 | Pro CCT 3 2 1 2 0 | His CAT 4 1 3 5 6 | Arg CGT 0 1 0 1 0 CTC 3 5 6 3 2 | CCC 1 3 4 1 3 | CAC 4 5 3 0 1 | CGC 0 2 3 0 1 CTA 0 0 0 0 0 | CCA 0 0 0 0 0 | Gln CAA 1 0 1 3 2 | CGA 0 0 0 0 0 CTG 6 12 11 6 7 | CCG 0 0 0 0 0 | CAG 4 5 4 4 3 | CGG 0 0 0 0 0 ---------------------------------------------------------------------------------------------------------------------- Ile ATT 1 0 1 5 2 | Thr ACT 5 2 3 4 3 | Asn AAT 2 1 1 4 4 | Ser AGT 1 0 0 3 2 ATC 4 7 6 2 2 | ACC 4 5 4 1 1 | AAC 3 6 6 4 2 | AGC 1 1 2 2 5 ATA 0 0 0 0 0 | ACA 0 1 0 1 1 | Lys AAA 0 1 1 3 6 | Arg AGA 0 0 0 1 0 Met ATG 3 1 1 0 0 | ACG 0 0 0 0 0 | AAG 12 9 9 8 5 | AGG 2 3 3 1 2 ---------------------------------------------------------------------------------------------------------------------- Val GTT 5 0 0 8 6 | Ala GCT 5 3 4 7 9 | Asp GAT 2 2 1 3 7 | Gly GGT 6 1 1 3 1 GTC 3 5 5 3 7 | GCC 6 14 11 9 3 | GAC 4 6 5 2 1 | GGC 3 4 4 5 3 GTA 0 0 0 2 0 | GCA 1 0 0 1 4 | Glu GAA 2 0 4 3 4 | GGA 1 2 0 4 4 GTG 5 6 6 3 5 | GCG 0 0 1 0 1 | GAG 6 5 3 3 2 | GGG 2 1 3 0 1 ---------------------------------------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: human position 1: T:0.12500 C:0.25000 A:0.20833 G:0.41667 position 2: T:0.30556 C:0.22222 A:0.31944 G:0.15278 position 3: T:0.28472 C:0.30556 A:0.05556 G:0.35417 Average T:0.23843 C:0.25926 A:0.19444 G:0.30787 #2: tarsier position 1: T:0.13889 C:0.20833 A:0.22222 G:0.43056 position 2: T:0.30556 C:0.22222 A:0.32639 G:0.14583 position 3: T:0.26389 C:0.33333 A:0.05556 G:0.34722 Average T:0.23611 C:0.25463 A:0.20139 G:0.30787 #3: bushbaby position 1: T:0.13194 C:0.25000 A:0.21528 G:0.40278 position 2: T:0.31250 C:0.20139 A:0.33333 G:0.15278 position 3: T:0.27083 C:0.31944 A:0.04167 G:0.36806 Average T:0.23843 C:0.25694 A:0.19676 G:0.30787 #4: hare position 1: T:0.13889 C:0.23611 A:0.22222 G:0.40278 position 2: T:0.31250 C:0.20833 A:0.32639 G:0.15278 position 3: T:0.27778 C:0.29167 A:0.05556 G:0.37500 Average T:0.24306 C:0.24537 A:0.20139 G:0.31019 #5: rabbit position 1: T:0.13889 C:0.23611 A:0.22917 G:0.39583 position 2: T:0.31250 C:0.20139 A:0.34028 G:0.14583 position 3: T:0.28472 C:0.27778 A:0.06250 G:0.37500 Average T:0.24537 C:0.23843 A:0.21065 G:0.30556 #6: cow position 1: T:0.13194 C:0.20833 A:0.22917 G:0.43056 position 2: T:0.32639 C:0.20139 A:0.33333 G:0.13889 position 3: T:0.30556 C:0.27778 A:0.04167 G:0.37500 Average T:0.25463 C:0.22917 A:0.20139 G:0.31481 #7: sheep position 1: T:0.11806 C:0.23611 A:0.22222 G:0.42361 position 2: T:0.31944 C:0.18056 A:0.36111 G:0.13889 position 3: T:0.27778 C:0.31944 A:0.03472 G:0.36806 Average T:0.23843 C:0.24537 A:0.20602 G:0.31019 #8: pig position 1: T:0.11806 C:0.25694 A:0.20139 G:0.42361 position 2: T:0.32639 C:0.16667 A:0.34722 G:0.15972 position 3: T:0.22917 C:0.38194 A:0.02778 G:0.36111 Average T:0.22454 C:0.26852 A:0.19213 G:0.31481 #9: elephseal position 1: T:0.15278 C:0.23611 A:0.24306 G:0.36806 position 2: T:0.31250 C:0.19444 A:0.34028 G:0.15278 position 3: T:0.24306 C:0.34028 A:0.04861 G:0.36806 Average T:0.23611 C:0.25694 A:0.21065 G:0.29630 #10: rat position 1: T:0.13194 C:0.22222 A:0.25000 G:0.39583 position 2: T:0.29861 C:0.20139 A:0.34028 G:0.15972 position 3: T:0.28472 C:0.33333 A:0.05556 G:0.32639 Average T:0.23843 C:0.25231 A:0.21528 G:0.29398 #11: mouse position 1: T:0.13194 C:0.22917 A:0.24306 G:0.39583 position 2: T:0.29167 C:0.23611 A:0.31944 G:0.15278 position 3: T:0.26389 C:0.35417 A:0.06944 G:0.31250 Average T:0.22917 C:0.27315 A:0.21065 G:0.28704 #12: hamster position 1: T:0.12500 C:0.25000 A:0.24306 G:0.38194 position 2: T:0.33333 C:0.20139 A:0.33333 G:0.13194 position 3: T:0.24306 C:0.37500 A:0.04861 G:0.33333 Average T:0.23380 C:0.27546 A:0.20833 G:0.28241 #13: marsupial position 1: T:0.19444 C:0.18750 A:0.26389 G:0.35417 position 2: T:0.29167 C:0.22222 A:0.32639 G:0.15972 position 3: T:0.32639 C:0.30556 A:0.04167 G:0.32639 Average T:0.27083 C:0.23843 A:0.21065 G:0.28009 #14: duck position 1: T:0.14583 C:0.25694 A:0.25694 G:0.34028 position 2: T:0.31250 C:0.23611 A:0.29861 G:0.15278 position 3: T:0.10417 C:0.54861 A:0.02778 G:0.31944 Average T:0.18750 C:0.34722 A:0.19444 G:0.27083 #15: chicken position 1: T:0.15278 C:0.25694 A:0.25694 G:0.33333 position 2: T:0.31250 C:0.22917 A:0.29861 G:0.15972 position 3: T:0.14583 C:0.50000 A:0.04167 G:0.31250 Average T:0.20370 C:0.32870 A:0.19907 G:0.26852 #16: xenlaev position 1: T:0.15278 C:0.18750 A:0.27083 G:0.38889 position 2: T:0.29861 C:0.22222 A:0.31250 G:0.16667 position 3: T:0.37500 C:0.27083 A:0.13889 G:0.21528 Average T:0.27546 C:0.22685 A:0.24074 G:0.25694 #17: xentrop position 1: T:0.13889 C:0.21528 A:0.24306 G:0.40278 position 2: T:0.29861 C:0.22222 A:0.31944 G:0.15972 position 3: T:0.35417 C:0.27778 A:0.15972 G:0.20833 Average T:0.26389 C:0.23843 A:0.24074 G:0.25694 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 65 | Ser S TCT 29 | Tyr Y TAT 12 | Cys C TGT 22 TTC 68 | TCC 44 | TAC 32 | TGC 6 Leu L TTA 1 | TCA 4 | *** * TAA 0 | *** * TGA 0 TTG 15 | TCG 0 | TAG 0 | Trp W TGG 43 ------------------------------------------------------------------------------ Leu L CTT 13 | Pro P CCT 40 | His H CAT 48 | Arg R CGT 2 CTC 54 | CCC 24 | CAC 78 | CGC 11 CTA 6 | CCA 9 | Gln Q CAA 7 | CGA 0 CTG 203 | CCG 4 | CAG 65 | CGG 1 ------------------------------------------------------------------------------ Ile I ATT 16 | Thr T ACT 45 | Asn N AAT 49 | Ser S AGT 31 ATC 28 | ACC 46 | AAC 70 | AGC 19 ATA 3 | ACA 4 | Lys K AAA 36 | Arg R AGA 2 Met M ATG 23 | ACG 1 | AAG 163 | AGG 43 ------------------------------------------------------------------------------ Val V GTT 62 | Ala A GCT 113 | Asp D GAT 57 | Gly G GGT 49 GTC 51 | GCC 132 | GAC 65 | GGC 109 GTA 4 | GCA 12 | Glu E GAA 40 | GGA 17 GTG 147 | GCG 7 | GAG 81 | GGG 17 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.13930 C:0.23080 A:0.23652 G:0.39338 position 2: T:0.31005 C:0.20997 A:0.32802 G:0.15196 position 3: T:0.26675 C:0.34191 A:0.05923 G:0.33211 Average T:0.23870 C:0.26089 A:0.20792 G:0.29248 TREE # 1: (16, 17, ((14, 15), (13, ((12, (10, 11)), ((9, (8, (6, 7))), ((3, (4, 5)), (1, 2))))))); MP score: 613 lnL(ntime: 31 np: 35): -3692.348587 +0.000000 18..16 18..17 18..19 19..20 20..14 20..15 19..21 21..13 21..22 22..23 23..12 23..24 24..10 24..11 22..25 25..26 26..9 26..27 27..8 27..28 28..6 28..7 25..29 29..30 30..3 30..31 31..4 31..5 29..32 32..1 32..2 0.496210 0.749157 1.815923 0.550885 0.177763 0.051672 0.199738 0.856081 0.322122 0.275739 0.359842 0.099315 0.133343 0.190760 0.050749 0.057706 0.216576 0.061037 0.313889 0.136267 0.060777 0.094396 0.070414 0.018595 0.145755 0.160680 0.026705 0.061188 0.060724 0.173559 0.215715 2.052093 0.895470 0.655552 3.243167 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 8.203279 (16: 0.496210, 17: 0.749157, ((14: 0.177763, 15: 0.051672): 0.550885, (13: 0.856081, ((12: 0.359842, (10: 0.133343, 11: 0.190760): 0.099315): 0.275739, ((9: 0.216576, (8: 0.313889, (6: 0.060777, 7: 0.094396): 0.136267): 0.061037): 0.057706, ((3: 0.145755, (4: 0.026705, 5: 0.061188): 0.160680): 0.018595, (1: 0.173559, 2: 0.215715): 0.060724): 0.070414): 0.050749): 0.322122): 0.199738): 1.815923); (xenlaev: 0.496210, xentrop: 0.749157, ((duck: 0.177763, chicken: 0.051672): 0.550885, (marsupial: 0.856081, ((hamster: 0.359842, (rat: 0.133343, mouse: 0.190760): 0.099315): 0.275739, ((elephseal: 0.216576, (pig: 0.313889, (cow: 0.060777, sheep: 0.094396): 0.136267): 0.061037): 0.057706, ((bushbaby: 0.145755, (hare: 0.026705, rabbit: 0.061188): 0.160680): 0.018595, (human: 0.173559, tarsier: 0.215715): 0.060724): 0.070414): 0.050749): 0.322122): 0.199738): 1.815923); Detailed output identifying parameters kappa (ts/tv) = 2.05209 Parameters in M8 (beta&w>1): p0 = 0.89547 p = 0.65555 q = 3.24317 (p1 = 0.10453) w = 1.00000 MLEs of dN/dS (w) for site classes (K=11) p: 0.08955 0.08955 0.08955 0.08955 0.08955 0.08955 0.08955 0.08955 0.08955 0.08955 0.10453 w: 0.00288 0.01567 0.03506 0.06066 0.09302 0.13353 0.18486 0.25229 0.34844 0.52272 1.00000 dN & dS for each branch branch t N S dN/dS dN dS N*dN S*dS 18..16 0.496 329.6 102.4 0.2522 0.0971 0.3851 32.0 39.4 18..17 0.749 329.6 102.4 0.2522 0.1466 0.5814 48.3 59.6 18..19 1.816 329.6 102.4 0.2522 0.3554 1.4092 117.1 144.4 19..20 0.551 329.6 102.4 0.2522 0.1078 0.4275 35.5 43.8 20..14 0.178 329.6 102.4 0.2522 0.0348 0.1380 11.5 14.1 20..15 0.052 329.6 102.4 0.2522 0.0101 0.0401 3.3 4.1 19..21 0.200 329.6 102.4 0.2522 0.0391 0.1550 12.9 15.9 21..13 0.856 329.6 102.4 0.2522 0.1676 0.6643 55.2 68.1 21..22 0.322 329.6 102.4 0.2522 0.0630 0.2500 20.8 25.6 22..23 0.276 329.6 102.4 0.2522 0.0540 0.2140 17.8 21.9 23..12 0.360 329.6 102.4 0.2522 0.0704 0.2792 23.2 28.6 23..24 0.099 329.6 102.4 0.2522 0.0194 0.0771 6.4 7.9 24..10 0.133 329.6 102.4 0.2522 0.0261 0.1035 8.6 10.6 24..11 0.191 329.6 102.4 0.2522 0.0373 0.1480 12.3 15.2 22..25 0.051 329.6 102.4 0.2522 0.0099 0.0394 3.3 4.0 25..26 0.058 329.6 102.4 0.2522 0.0113 0.0448 3.7 4.6 26..9 0.217 329.6 102.4 0.2522 0.0424 0.1681 14.0 17.2 26..27 0.061 329.6 102.4 0.2522 0.0119 0.0474 3.9 4.9 27..8 0.314 329.6 102.4 0.2522 0.0614 0.2436 20.2 25.0 27..28 0.136 329.6 102.4 0.2522 0.0267 0.1057 8.8 10.8 28..6 0.061 329.6 102.4 0.2522 0.0119 0.0472 3.9 4.8 28..7 0.094 329.6 102.4 0.2522 0.0185 0.0733 6.1 7.5 25..29 0.070 329.6 102.4 0.2522 0.0138 0.0546 4.5 5.6 29..30 0.019 329.6 102.4 0.2522 0.0036 0.0144 1.2 1.5 30..3 0.146 329.6 102.4 0.2522 0.0285 0.1131 9.4 11.6 30..31 0.161 329.6 102.4 0.2522 0.0314 0.1247 10.4 12.8 31..4 0.027 329.6 102.4 0.2522 0.0052 0.0207 1.7 2.1 31..5 0.061 329.6 102.4 0.2522 0.0120 0.0475 3.9 4.9 29..32 0.061 329.6 102.4 0.2522 0.0119 0.0471 3.9 4.8 32..1 0.174 329.6 102.4 0.2522 0.0340 0.1347 11.2 13.8 32..2 0.216 329.6 102.4 0.2522 0.0422 0.1674 13.9 17.1 Naive Empirical Bayes (NEB) analysis Time used: 3:58