seed used = 748812793 CODONML (in paml version 4.3b, February 2009) codon.filter Model: free dN/dS Ratios for branches for branches Codon frequency model: F3x4 ns = 8 ls = 81 Codon usage in sequences -------------------------------------------------------------------------------------------------------------- Phe TTT 1 1 1 2 2 1 | Ser TCT 2 2 2 2 2 2 | Tyr TAT 0 0 0 0 0 0 | Cys TGT 1 1 1 1 1 1 TTC 1 1 1 1 0 1 | TCC 4 4 4 4 4 4 | TAC 2 2 2 2 2 2 | TGC 0 0 0 0 0 0 Leu TTA 2 2 2 2 2 1 | TCA 1 1 1 1 1 1 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 3 3 3 3 4 5 | TCG 0 0 0 0 0 1 | TAG 0 0 0 0 0 0 | Trp TGG 4 4 4 4 4 4 -------------------------------------------------------------------------------------------------------------- Leu CTT 2 2 2 2 3 1 | Pro CCT 0 0 0 0 0 1 | His CAT 0 0 0 0 0 0 | Arg CGT 0 0 0 0 1 0 CTC 1 1 1 1 1 2 | CCC 1 1 1 1 2 1 | CAC 0 0 0 0 0 0 | CGC 0 0 0 0 0 0 CTA 1 1 1 1 1 0 | CCA 1 1 1 2 0 0 | Gln CAA 2 2 2 2 3 2 | CGA 0 0 0 0 0 0 CTG 2 2 2 2 1 2 | CCG 1 1 1 0 1 0 | CAG 3 3 3 3 2 2 | CGG 0 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------- Ile ATT 1 1 1 0 1 1 | Thr ACT 0 0 0 0 1 0 | Asn AAT 0 0 0 0 0 1 | Ser AGT 0 0 0 0 0 0 ATC 1 1 1 1 1 1 | ACC 1 1 1 1 0 1 | AAC 3 3 3 3 3 3 | AGC 0 0 0 0 0 0 ATA 0 0 0 0 0 0 | ACA 0 0 0 0 0 0 | Lys AAA 1 1 1 1 2 1 | Arg AGA 3 3 3 3 3 2 Met ATG 6 7 6 6 5 6 | ACG 0 0 0 0 0 0 | AAG 5 5 5 5 2 3 | AGG 1 1 1 1 1 2 -------------------------------------------------------------------------------------------------------------- Val GTT 0 0 0 0 1 1 | Ala GCT 1 1 1 1 3 2 | Asp GAT 3 3 3 3 3 4 | Gly GGT 0 0 0 0 0 0 GTC 1 1 1 1 1 1 | GCC 1 1 1 1 0 1 | GAC 1 1 1 1 1 1 | GGC 0 0 0 0 0 0 GTA 1 1 1 2 1 2 | GCA 0 0 0 1 0 0 | Glu GAA 3 3 3 3 2 4 | GGA 1 1 1 2 2 3 GTG 4 3 4 3 3 2 | GCG 1 1 1 0 0 0 | GAG 4 4 4 4 6 4 | GGG 3 3 3 2 2 1 -------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------- Phe TTT 1 1 | Ser TCT 4 4 | Tyr TAT 0 0 | Cys TGT 1 1 TTC 1 1 | TCC 2 2 | TAC 2 2 | TGC 0 0 Leu TTA 1 2 | TCA 1 1 | *** TAA 0 0 | *** TGA 0 0 TTG 5 3 | TCG 0 0 | TAG 0 0 | Trp TGG 4 5 -------------------------------------------------------------- Leu CTT 2 2 | Pro CCT 0 1 | His CAT 0 0 | Arg CGT 0 0 CTC 1 1 | CCC 2 1 | CAC 0 0 | CGC 0 0 CTA 0 0 | CCA 1 1 | Gln CAA 3 2 | CGA 0 0 CTG 2 2 | CCG 0 0 | CAG 1 2 | CGG 0 0 -------------------------------------------------------------- Ile ATT 1 1 | Thr ACT 0 0 | Asn AAT 0 0 | Ser AGT 0 0 ATC 1 1 | ACC 1 1 | AAC 3 2 | AGC 0 1 ATA 0 1 | ACA 0 1 | Lys AAA 2 2 | Arg AGA 2 2 Met ATG 6 5 | ACG 0 0 | AAG 3 1 | AGG 1 2 -------------------------------------------------------------- Val GTT 1 1 | Ala GCT 2 2 | Asp GAT 5 5 | Gly GGT 1 0 GTC 1 1 | GCC 1 1 | GAC 1 1 | GGC 0 0 GTA 1 2 | GCA 0 0 | Glu GAA 3 3 | GGA 2 2 GTG 3 2 | GCG 0 0 | GAG 5 5 | GGG 1 2 -------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: hg18 position 1: T:0.25926 C:0.17284 A:0.27160 G:0.29630 position 2: T:0.33333 C:0.17284 A:0.33333 G:0.16049 position 3: T:0.13580 C:0.20988 A:0.19753 G:0.45679 Average T:0.24280 C:0.18519 A:0.26749 G:0.30453 #2: panTro2 position 1: T:0.25926 C:0.17284 A:0.28395 G:0.28395 position 2: T:0.33333 C:0.17284 A:0.33333 G:0.16049 position 3: T:0.13580 C:0.20988 A:0.19753 G:0.45679 Average T:0.24280 C:0.18519 A:0.27160 G:0.30041 #3: ponAbe2 position 1: T:0.25926 C:0.17284 A:0.27160 G:0.29630 position 2: T:0.33333 C:0.17284 A:0.33333 G:0.16049 position 3: T:0.13580 C:0.20988 A:0.19753 G:0.45679 Average T:0.24280 C:0.18519 A:0.26749 G:0.30453 #4: calJac1 position 1: T:0.27160 C:0.17284 A:0.25926 G:0.29630 position 2: T:0.33333 C:0.17284 A:0.33333 G:0.16049 position 3: T:0.13580 C:0.20988 A:0.24691 G:0.40741 Average T:0.24691 C:0.18519 A:0.27984 G:0.28807 #5: cavPor3 position 1: T:0.27160 C:0.18519 A:0.23457 G:0.30864 position 2: T:0.33333 C:0.17284 A:0.32099 G:0.17284 position 3: T:0.22222 C:0.18519 A:0.20988 G:0.38272 Average T:0.27572 C:0.18107 A:0.25514 G:0.28807 #6: bosTau4 position 1: T:0.28395 C:0.13580 A:0.25926 G:0.32099 position 2: T:0.33333 C:0.17284 A:0.33333 G:0.16049 position 3: T:0.18519 C:0.22222 A:0.19753 G:0.39506 Average T:0.26749 C:0.17695 A:0.26337 G:0.29218 #7: canFam2 position 1: T:0.27160 C:0.14815 A:0.24691 G:0.33333 position 2: T:0.33333 C:0.17284 A:0.34568 G:0.14815 position 3: T:0.22222 C:0.19753 A:0.19753 G:0.38272 Average T:0.27572 C:0.17284 A:0.26337 G:0.28807 #8: dasNov2 position 1: T:0.27160 C:0.14815 A:0.24691 G:0.33333 position 2: T:0.32099 C:0.18519 A:0.30864 G:0.18519 position 3: T:0.22222 C:0.18519 A:0.23457 G:0.35802 Average T:0.27160 C:0.17284 A:0.26337 G:0.29218 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 10 | Ser S TCT 20 | Tyr Y TAT 0 | Cys C TGT 8 TTC 7 | TCC 28 | TAC 16 | TGC 0 Leu L TTA 14 | TCA 8 | *** * TAA 0 | *** * TGA 0 TTG 29 | TCG 1 | TAG 0 | Trp W TGG 33 ------------------------------------------------------------------------------ Leu L CTT 16 | Pro P CCT 2 | His H CAT 0 | Arg R CGT 1 CTC 9 | CCC 10 | CAC 0 | CGC 0 CTA 5 | CCA 7 | Gln Q CAA 18 | CGA 0 CTG 15 | CCG 4 | CAG 19 | CGG 0 ------------------------------------------------------------------------------ Ile I ATT 7 | Thr T ACT 1 | Asn N AAT 1 | Ser S AGT 0 ATC 8 | ACC 7 | AAC 23 | AGC 1 ATA 1 | ACA 1 | Lys K AAA 11 | Arg R AGA 21 Met M ATG 47 | ACG 0 | AAG 29 | AGG 10 ------------------------------------------------------------------------------ Val V GTT 4 | Ala A GCT 13 | Asp D GAT 29 | Gly G GGT 1 GTC 8 | GCC 7 | GAC 8 | GGC 0 GTA 11 | GCA 1 | Glu E GAA 24 | GGA 14 GTG 24 | GCG 3 | GAG 36 | GGG 17 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.26852 C:0.16358 A:0.25926 G:0.30864 position 2: T:0.33179 C:0.17438 A:0.33025 G:0.16358 position 3: T:0.17438 C:0.20370 A:0.20988 G:0.41204 Average T:0.25823 C:0.18056 A:0.26646 G:0.29475 TREE # 1: ((((((1, 2), 3), 4), 5), (7, 6)), 8); MP score: 64 This is a rooted tree. Please check! lnL(ntime: 14 np: 29): -634.148257 +0.000000 9..10 10..11 11..12 12..13 13..14 14..1 14..2 13..3 12..4 11..5 10..15 15..7 15..6 9..8 0.184938 0.012799 0.142255 0.034129 0.000004 0.000004 0.012023 0.000004 0.033040 0.204560 0.071334 0.120778 0.149625 0.034590 3.804885 0.373462 999.000000 0.212211 0.000100 0.000100 0.000100 999.000000 0.000100 0.231777 0.247101 0.000100 0.044880 0.078269 999.000000 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 1.00008 ((((((1: 0.000004, 2: 0.012023): 0.000004, 3: 0.000004): 0.034129, 4: 0.033040): 0.142255, 5: 0.204560): 0.012799, (7: 0.120778, 6: 0.149625): 0.071334): 0.184938, 8: 0.034590); ((((((hg18: 0.000004, panTro2: 0.012023): 0.000004, ponAbe2: 0.000004): 0.034129, calJac1: 0.033040): 0.142255, cavPor3: 0.204560): 0.012799, (canFam2: 0.120778, bosTau4: 0.149625): 0.071334): 0.184938, dasNov2: 0.034590); Detailed output identifying parameters kappa (ts/tv) = 3.80488 w (dN/dS) for branches: 0.37346 999.00000 0.21221 0.00010 0.00010 0.00010 999.00000 0.00010 0.23178 0.24710 0.00010 0.04488 0.07827 999.00000 dN & dS for each branch branch t N S dN/dS dN dS N*dN S*dS 9..10 0.185 175.6 67.4 0.3735 0.0421 0.1126 7.4 7.6 10..11 0.013 175.6 67.4 999.0000 0.0059 0.0000 1.0 0.0 11..12 0.142 175.6 67.4 0.2122 0.0234 0.1101 4.1 7.4 12..13 0.034 175.6 67.4 0.0001 0.0000 0.0410 0.0 2.8 13..14 0.000 175.6 67.4 0.0001 0.0000 0.0000 0.0 0.0 14..1 0.000 175.6 67.4 0.0001 0.0000 0.0000 0.0 0.0 14..2 0.012 175.6 67.4 999.0000 0.0055 0.0000 1.0 0.0 13..3 0.000 175.6 67.4 0.0001 0.0000 0.0000 0.0 0.0 12..4 0.033 175.6 67.4 0.2318 0.0057 0.0248 1.0 1.7 11..5 0.205 175.6 67.4 0.2471 0.0370 0.1495 6.5 10.1 10..15 0.071 175.6 67.4 0.0001 0.0000 0.0857 0.0 5.8 15..7 0.121 175.6 67.4 0.0449 0.0058 0.1299 1.0 8.8 15..6 0.150 175.6 67.4 0.0783 0.0117 0.1493 2.1 10.1 9..8 0.035 175.6 67.4 999.0000 0.0160 0.0000 2.8 0.0 tree length for dN: 0.1530 tree length for dS: 0.8030 dS tree: ((((((hg18: 0.000005, panTro2: 0.000006): 0.000005, ponAbe2: 0.000005): 0.040997, calJac1: 0.024754): 0.110079, cavPor3: 0.149541): 0.000006, (canFam2: 0.129930, bosTau4: 0.149335): 0.085688): 0.112641, dasNov2: 0.000016); dN tree: ((((((hg18: 0.000000, panTro2: 0.005544): 0.000000, ponAbe2: 0.000000): 0.000004, calJac1: 0.005737): 0.023360, cavPor3: 0.036952): 0.005902, (canFam2: 0.005831, bosTau4: 0.011688): 0.000009): 0.042067, dasNov2: 0.015951); w ratios as labels for TreeView: ((((((hg18 '#0.0001' , panTro2 '#999.0000' ) '#0.0001' , ponAbe2 '#0.0001' ) '#0.0001' , calJac1 '#0.2318' ) '#0.2122' , cavPor3 '#0.2471' ) '#999.0000' , (canFam2 '#0.0449' , bosTau4 '#0.0783' ) '#0.0001' ) '#0.3735' , dasNov2 '#999.0000' ); Time used: 2:42