CODONML (in paml version 4.10.0, September 2020) HIVenvSweden.phy Model: One dN/dS ratio, Codon frequency model: F3x4 ns = 13 ls = 91 Codon usage in sequences -------------------------------------------------------------------------------------------------------------------------------------- Phe TTT 4 3 2 2 2 3 | Ser TCT 2 2 2 2 2 1 | Tyr TAT 2 2 2 2 1 1 | Cys TGT 2 2 2 2 2 2 TTC 1 2 1 1 1 1 | TCC 1 1 1 1 1 1 | TAC 0 0 0 0 1 0 | TGC 0 0 0 0 0 0 Leu TTA 2 1 2 2 2 2 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 0 0 0 0 0 0 | TCG 1 1 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------------------------------- Leu CTT 1 1 1 1 0 1 | Pro CCT 0 0 0 0 0 1 | His CAT 1 1 2 2 3 2 | Arg CGT 0 0 0 0 0 0 CTC 0 0 0 0 0 0 | CCC 1 1 1 1 1 1 | CAC 0 0 0 0 0 0 | CGC 0 0 0 0 0 0 CTA 1 1 1 1 1 1 | CCA 1 1 1 1 1 2 | Gln CAA 3 3 3 3 3 3 | CGA 0 0 0 0 0 0 CTG 0 0 0 0 0 1 | CCG 0 0 0 0 0 0 | CAG 2 2 2 2 1 1 | CGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------------------------------- Ile ATT 3 2 2 2 4 2 | Thr ACT 1 2 1 1 1 1 | Asn AAT 7 8 7 5 6 8 | Ser AGT 1 1 2 2 2 1 ATC 0 1 0 0 0 0 | ACC 2 1 1 1 1 1 | AAC 5 5 4 5 5 6 | AGC 0 0 0 0 0 0 ATA 7 8 7 8 7 8 | ACA 4 3 5 4 4 4 | Lys AAA 6 6 5 6 5 6 | Arg AGA 6 6 8 6 7 7 Met ATG 0 0 0 0 1 0 | ACG 0 0 1 1 2 1 | AAG 0 0 0 1 0 1 | AGG 0 0 0 1 0 0 -------------------------------------------------------------------------------------------------------------------------------------- Val GTT 1 0 0 0 0 0 | Ala GCT 2 2 2 2 2 2 | Asp GAT 1 1 1 1 1 0 | Gly GGT 0 0 0 0 0 0 GTC 0 0 1 1 1 1 | GCC 0 0 0 0 0 0 | GAC 0 0 1 0 0 1 | GGC 0 0 1 0 0 0 GTA 5 5 7 5 5 5 | GCA 3 5 2 2 2 3 | Glu GAA 6 5 5 8 8 4 | GGA 4 4 3 4 3 3 GTG 0 0 0 0 0 0 | GCG 0 0 0 0 0 0 | GAG 0 0 0 0 0 0 | GGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------------- Phe TTT 3 3 3 3 4 3 | Ser TCT 2 1 2 2 2 2 | Tyr TAT 1 1 1 2 1 1 | Cys TGT 2 2 2 2 2 2 TTC 1 1 1 1 1 1 | TCC 1 1 1 1 1 1 | TAC 0 0 0 0 0 0 | TGC 0 0 0 0 0 0 Leu TTA 2 2 3 2 2 2 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 0 0 0 0 0 0 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------------------------------- Leu CTT 1 1 1 1 1 1 | Pro CCT 1 1 0 0 0 0 | His CAT 1 2 2 1 1 1 | Arg CGT 0 0 0 0 0 0 CTC 0 0 0 0 0 0 | CCC 1 1 1 1 1 1 | CAC 0 0 0 0 0 0 | CGC 0 0 0 0 0 0 CTA 1 1 1 1 2 1 | CCA 1 1 1 1 1 1 | Gln CAA 3 2 5 5 4 4 | CGA 0 1 0 0 0 1 CTG 0 0 0 0 0 0 | CCG 0 0 0 0 0 0 | CAG 2 2 1 1 1 1 | CGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------------------------------- Ile ATT 2 2 2 2 2 2 | Thr ACT 1 2 1 1 1 1 | Asn AAT 5 4 7 6 9 6 | Ser AGT 2 1 2 2 2 2 ATC 1 0 0 0 0 0 | ACC 1 2 1 1 1 1 | AAC 6 5 4 5 4 5 | AGC 0 1 0 0 0 0 ATA 7 8 7 9 6 7 | ACA 4 4 7 6 6 5 | Lys AAA 2 7 5 5 6 6 | Arg AGA 9 6 8 8 8 8 Met ATG 0 0 0 0 0 0 | ACG 1 1 0 0 1 1 | AAG 3 2 0 0 0 0 | AGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------------------------------- Val GTT 1 1 1 0 1 0 | Ala GCT 1 1 3 2 2 3 | Asp GAT 1 1 1 1 0 1 | Gly GGT 0 0 1 0 1 0 GTC 0 0 0 1 0 1 | GCC 1 0 0 0 0 0 | GAC 3 1 1 2 1 1 | GGC 0 0 0 0 0 0 GTA 5 4 4 4 4 6 | GCA 2 4 2 3 3 3 | Glu GAA 3 6 5 4 5 5 | GGA 5 4 2 3 2 2 GTG 0 0 0 0 0 0 | GCG 0 0 0 0 0 0 | GAG 0 0 0 0 0 0 | GGG 1 0 1 1 1 1 -------------------------------------------------------------------------------------------------------------------------------------- ------------------------------------------------------ Phe TTT 2 | Ser TCT 1 | Tyr TAT 1 | Cys TGT 2 TTC 1 | TCC 1 | TAC 0 | TGC 0 Leu TTA 2 | TCA 0 | *** TAA 0 | *** TGA 0 TTG 0 | TCG 1 | TAG 0 | Trp TGG 1 ------------------------------------------------------ Leu CTT 1 | Pro CCT 0 | His CAT 2 | Arg CGT 0 CTC 0 | CCC 1 | CAC 0 | CGC 0 CTA 1 | CCA 1 | Gln CAA 3 | CGA 0 CTG 0 | CCG 0 | CAG 1 | CGG 0 ------------------------------------------------------ Ile ATT 1 | Thr ACT 4 | Asn AAT 6 | Ser AGT 1 ATC 2 | ACC 1 | AAC 7 | AGC 0 ATA 8 | ACA 5 | Lys AAA 6 | Arg AGA 7 Met ATG 0 | ACG 0 | AAG 0 | AGG 1 ------------------------------------------------------ Val GTT 1 | Ala GCT 2 | Asp GAT 1 | Gly GGT 0 GTC 0 | GCC 0 | GAC 1 | GGC 0 GTA 4 | GCA 2 | Glu GAA 5 | GGA 3 GTG 0 | GCG 0 | GAG 0 | GGG 1 ------------------------------------------------------ Codon position x base (3x4) table for each sequence. #1: U68496 position 1: T:0.17582 C:0.10989 A:0.46154 G:0.25275 position 2: T:0.27473 C:0.19780 A:0.36264 G:0.16484 position 3: T:0.30769 C:0.10989 A:0.52747 G:0.05495 Average T:0.25275 C:0.13919 A:0.45055 G:0.15751 #2: U68497 position 1: T:0.16484 C:0.10989 A:0.47253 G:0.25275 position 2: T:0.26374 C:0.20879 A:0.36264 G:0.16484 position 3: T:0.29670 C:0.12088 A:0.52747 G:0.05495 Average T:0.24176 C:0.14652 A:0.45421 G:0.15751 #3: U68498 position 1: T:0.14286 C:0.12088 A:0.47253 G:0.26374 position 2: T:0.26374 C:0.18681 A:0.35165 G:0.19780 position 3: T:0.28571 C:0.12088 A:0.53846 G:0.05495 Average T:0.23077 C:0.14286 A:0.45421 G:0.17216 #4: U68499 position 1: T:0.14286 C:0.12088 A:0.47253 G:0.26374 position 2: T:0.25275 C:0.17582 A:0.38462 G:0.18681 position 3: T:0.26374 C:0.10989 A:0.54945 G:0.07692 Average T:0.21978 C:0.13553 A:0.46886 G:0.17582 #5: U68500 position 1: T:0.14286 C:0.10989 A:0.49451 G:0.25275 position 2: T:0.26374 C:0.18681 A:0.37363 G:0.17582 position 3: T:0.28571 C:0.12088 A:0.52747 G:0.06593 Average T:0.23077 C:0.13919 A:0.46520 G:0.16484 #6: U68501 position 1: T:0.13187 C:0.14286 A:0.50549 G:0.21978 position 2: T:0.27473 C:0.19780 A:0.36264 G:0.16484 position 3: T:0.27473 C:0.13187 A:0.52747 G:0.06593 Average T:0.22711 C:0.15751 A:0.46520 G:0.15018 #7: U68502 position 1: T:0.14286 C:0.12088 A:0.48352 G:0.25275 position 2: T:0.26374 C:0.18681 A:0.32967 G:0.21978 position 3: T:0.26374 C:0.16484 A:0.48352 G:0.08791 Average T:0.22344 C:0.15751 A:0.43223 G:0.18681 #8: U68503 position 1: T:0.13187 C:0.13187 A:0.49451 G:0.24176 position 2: T:0.25275 C:0.20879 A:0.36264 G:0.17582 position 3: T:0.25275 C:0.13187 A:0.54945 G:0.06593 Average T:0.21245 C:0.15751 A:0.46886 G:0.16117 #9: U68504 position 1: T:0.15385 C:0.13187 A:0.48352 G:0.23077 position 2: T:0.25275 C:0.20879 A:0.35165 G:0.18681 position 3: T:0.31868 C:0.09890 A:0.54945 G:0.03297 Average T:0.24176 C:0.14652 A:0.46154 G:0.15018 #10: U68505 position 1: T:0.15385 C:0.12088 A:0.49451 G:0.23077 position 2: T:0.26374 C:0.19780 A:0.35165 G:0.18681 position 3: T:0.27473 C:0.13187 A:0.56044 G:0.03297 Average T:0.23077 C:0.15018 A:0.46886 G:0.15018 #11: U68506 position 1: T:0.15385 C:0.12088 A:0.50549 G:0.21978 position 2: T:0.25275 C:0.20879 A:0.35165 G:0.18681 position 3: T:0.31868 C:0.09890 A:0.53846 G:0.04396 Average T:0.24176 C:0.14286 A:0.46520 G:0.15018 #12: U68507 position 1: T:0.14286 C:0.12088 A:0.48352 G:0.25275 position 2: T:0.26374 C:0.20879 A:0.34066 G:0.18681 position 3: T:0.27473 C:0.12088 A:0.56044 G:0.04396 Average T:0.22711 C:0.15018 A:0.46154 G:0.16117 #13: U68508 position 1: T:0.13187 C:0.10989 A:0.53846 G:0.21978 position 2: T:0.25275 C:0.20879 A:0.36264 G:0.17582 position 3: T:0.27473 C:0.15385 A:0.51648 G:0.05495 Average T:0.21978 C:0.15751 A:0.47253 G:0.15018 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 37 | Ser S TCT 23 | Tyr Y TAT 18 | Cys C TGT 26 TTC 14 | TCC 13 | TAC 1 | TGC 0 Leu L TTA 26 | TCA 0 | *** * TAA 0 | *** * TGA 0 TTG 0 | TCG 3 | TAG 0 | Trp W TGG 13 ------------------------------------------------------------------------------ Leu L CTT 12 | Pro P CCT 3 | His H CAT 21 | Arg R CGT 0 CTC 0 | CCC 13 | CAC 0 | CGC 0 CTA 14 | CCA 14 | Gln Q CAA 44 | CGA 2 CTG 1 | CCG 0 | CAG 19 | CGG 0 ------------------------------------------------------------------------------ Ile I ATT 28 | Thr T ACT 18 | Asn N AAT 84 | Ser S AGT 21 ATC 4 | ACC 15 | AAC 66 | AGC 1 ATA 97 | ACA 61 | Lys K AAA 71 | Arg R AGA 94 Met M ATG 1 | ACG 9 | AAG 7 | AGG 2 ------------------------------------------------------------------------------ Val V GTT 6 | Ala A GCT 26 | Asp D GAT 11 | Gly G GGT 2 GTC 6 | GCC 1 | GAC 12 | GGC 1 GTA 63 | GCA 36 | Glu E GAA 69 | GGA 42 GTG 0 | GCG 0 | GAG 0 | GGG 12 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.14708 C:0.12088 A:0.48943 G:0.24260 position 2: T:0.26120 C:0.19865 A:0.35757 G:0.18259 position 3: T:0.28402 C:0.12426 A:0.53508 G:0.05664 Average T:0.23077 C:0.14793 A:0.46069 G:0.16061 TREE # 1: (1, 2, ((3, (4, 5)), (6, (7, (8, ((((9, 11), 10), 12), 13)))))); MP score: 136 lnL(ntime: 23 np: 25): -1137.688190 +0.000000 14..1 14..2 14..15 15..16 16..3 16..17 17..4 17..5 15..18 18..6 18..19 19..7 19..20 20..8 20..21 21..22 22..23 23..24 24..9 24..11 23..10 22..12 21..13 0.023746 0.079178 0.152813 0.023647 0.050407 0.083460 0.028429 0.099890 0.048101 0.131681 0.033695 0.191150 0.064013 0.193336 0.050591 0.034773 0.036688 0.055603 0.018984 0.070370 0.030301 0.061120 0.198346 2.471747 0.901293 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 1.760324 (1: 0.023746, 2: 0.079178, ((3: 0.050407, (4: 0.028429, 5: 0.099890): 0.083460): 0.023647, (6: 0.131681, (7: 0.191150, (8: 0.193336, ((((9: 0.018984, 11: 0.070370): 0.055603, 10: 0.030301): 0.036688, 12: 0.061120): 0.034773, 13: 0.198346): 0.050591): 0.064013): 0.033695): 0.048101): 0.152813); (U68496: 0.023746, U68497: 0.079178, ((U68498: 0.050407, (U68499: 0.028429, U68500: 0.099890): 0.083460): 0.023647, (U68501: 0.131681, (U68502: 0.191150, (U68503: 0.193336, ((((U68504: 0.018984, U68506: 0.070370): 0.055603, U68505: 0.030301): 0.036688, U68507: 0.061120): 0.034773, U68508: 0.198346): 0.050591): 0.064013): 0.033695): 0.048101): 0.152813); Detailed output identifying parameters kappa (ts/tv) = 2.47175 omega (dN/dS) = 0.90129 dN & dS for each branch branch t N S dN/dS dN dS N*dN S*dS 14..1 0.024 231.1 41.9 0.9013 0.0078 0.0086 1.8 0.4 14..2 0.079 231.1 41.9 0.9013 0.0260 0.0288 6.0 1.2 14..15 0.153 231.1 41.9 0.9013 0.0501 0.0556 11.6 2.3 15..16 0.024 231.1 41.9 0.9013 0.0078 0.0086 1.8 0.4 16..3 0.050 231.1 41.9 0.9013 0.0165 0.0183 3.8 0.8 16..17 0.083 231.1 41.9 0.9013 0.0274 0.0304 6.3 1.3 17..4 0.028 231.1 41.9 0.9013 0.0093 0.0103 2.2 0.4 17..5 0.100 231.1 41.9 0.9013 0.0327 0.0363 7.6 1.5 15..18 0.048 231.1 41.9 0.9013 0.0158 0.0175 3.6 0.7 18..6 0.132 231.1 41.9 0.9013 0.0432 0.0479 10.0 2.0 18..19 0.034 231.1 41.9 0.9013 0.0110 0.0123 2.6 0.5 19..7 0.191 231.1 41.9 0.9013 0.0627 0.0695 14.5 2.9 19..20 0.064 231.1 41.9 0.9013 0.0210 0.0233 4.8 1.0 20..8 0.193 231.1 41.9 0.9013 0.0634 0.0703 14.6 2.9 20..21 0.051 231.1 41.9 0.9013 0.0166 0.0184 3.8 0.8 21..22 0.035 231.1 41.9 0.9013 0.0114 0.0126 2.6 0.5 22..23 0.037 231.1 41.9 0.9013 0.0120 0.0133 2.8 0.6 23..24 0.056 231.1 41.9 0.9013 0.0182 0.0202 4.2 0.8 24..9 0.019 231.1 41.9 0.9013 0.0062 0.0069 1.4 0.3 24..11 0.070 231.1 41.9 0.9013 0.0231 0.0256 5.3 1.1 23..10 0.030 231.1 41.9 0.9013 0.0099 0.0110 2.3 0.5 22..12 0.061 231.1 41.9 0.9013 0.0200 0.0222 4.6 0.9 21..13 0.198 231.1 41.9 0.9013 0.0650 0.0721 15.0 3.0 tree length for dN: 0.5771 tree length for dS: 0.6403 Time used: 0:10