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CODONML (in paml version 4.6, August 2012) ../Alignments/lysinYangSwanson2002.nuc
Model: One dN/dS ratio for branches, (2 genes: diff. rate)
Codon frequency model: F3x4
ns = 25 ls = 134
Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 3 3 3 3 3 3 | Ser TCT 1 1 1 1 0 0 | Tyr TAT 2 2 1 2 3 3 | Cys TGT 0 0 0 0 0 0
TTC 3 3 3 3 3 4 | TCC 0 0 0 0 0 0 | TAC 8 8 8 7 6 5 | TGC 0 0 0 0 0 0
Leu TTA 2 2 1 2 1 1 | TCA 0 0 1 1 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
TTG 1 1 1 1 1 1 | TCG 0 1 1 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 4 4 4 5 4 4
--------------------------------------------------------------------------------------------------------------
Leu CTT 1 1 1 1 2 2 | Pro CCT 0 0 0 0 0 0 | His CAT 2 2 1 0 3 2 | Arg CGT 2 2 2 2 2 2
CTC 1 1 1 1 1 1 | CCC 1 1 1 1 1 0 | CAC 1 2 2 2 1 1 | CGC 2 3 3 2 2 2
CTA 0 0 0 0 0 0 | CCA 4 5 3 5 5 5 | Gln CAA 0 0 0 1 1 0 | CGA 0 0 0 1 0 1
CTG 6 6 6 5 5 5 | CCG 1 0 0 0 0 0 | CAG 3 3 3 3 4 4 | CGG 1 1 1 1 1 1
--------------------------------------------------------------------------------------------------------------
Ile ATT 4 4 5 4 3 3 | Thr ACT 1 2 1 2 2 2 | Asn AAT 4 3 5 5 4 5 | Ser AGT 0 0 0 0 0 0
ATC 3 3 4 3 4 4 | ACC 2 2 1 2 1 1 | AAC 2 4 3 2 3 5 | AGC 1 0 0 1 0 1
ATA 1 1 0 1 1 0 | ACA 2 2 2 0 0 0 | Lys AAA 4 4 3 4 4 4 | Arg AGA 7 6 8 7 9 9
Met ATG 7 7 6 8 7 6 | ACG 0 1 1 0 1 1 | AAG 8 7 6 8 6 5 | AGG 0 1 2 1 1 2
--------------------------------------------------------------------------------------------------------------
Val GTT 7 6 5 9 7 5 | Ala GCT 3 2 4 1 2 4 | Asp GAT 5 5 4 4 4 6 | Gly GGT 2 2 1 2 3 2
GTC 3 2 2 1 3 1 | GCC 1 1 1 2 1 2 | GAC 2 1 2 1 3 1 | GGC 2 2 2 2 2 2
GTA 1 1 3 0 1 2 | GCA 3 3 4 3 2 3 | Glu GAA 5 4 4 3 5 3 | GGA 2 3 3 2 2 2
GTG 0 0 0 0 0 2 | GCG 2 2 2 3 2 2 | GAG 0 0 1 2 1 1 | GGG 1 1 0 1 0 0
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
Phe TTT 3 3 3 3 4 4 | Ser TCT 0 0 0 1 0 0 | Tyr TAT 3 3 4 4 0 1 | Cys TGT 0 0 0 0 0 0
TTC 4 4 3 4 1 1 | TCC 0 0 0 1 2 0 | TAC 5 6 6 5 7 7 | TGC 0 0 0 0 0 0
Leu TTA 1 1 0 1 1 0 | TCA 0 0 0 0 1 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
TTG 1 1 3 2 4 4 | TCG 0 0 0 0 0 1 | TAG 0 0 0 0 0 0 | Trp TGG 4 3 3 4 5 4
--------------------------------------------------------------------------------------------------------------
Leu CTT 2 1 2 1 3 3 | Pro CCT 0 1 1 0 3 2 | His CAT 2 2 2 2 3 2 | Arg CGT 2 4 3 3 5 4
CTC 1 1 1 2 0 0 | CCC 0 0 0 1 1 2 | CAC 1 1 1 1 3 2 | CGC 2 4 4 2 2 2
CTA 0 0 0 0 0 0 | CCA 5 5 4 3 1 2 | Gln CAA 0 0 2 0 3 3 | CGA 1 0 1 2 0 2
CTG 5 6 5 4 2 2 | CCG 0 1 1 1 0 0 | CAG 4 3 4 5 6 4 | CGG 1 1 0 1 0 0
--------------------------------------------------------------------------------------------------------------
Ile ATT 3 5 4 1 3 3 | Thr ACT 2 0 0 3 1 1 | Asn AAT 5 3 9 5 1 2 | Ser AGT 0 2 0 0 0 0
ATC 4 2 2 3 4 4 | ACC 1 2 2 2 1 2 | AAC 5 4 3 3 3 2 | AGC 1 0 0 1 3 4
ATA 0 2 1 3 2 1 | ACA 0 1 0 1 0 0 | Lys AAA 4 2 3 3 3 3 | Arg AGA 8 6 7 7 3 4
Met ATG 6 6 6 6 4 4 | ACG 1 1 1 1 1 1 | AAG 5 6 5 7 4 5 | AGG 2 2 2 1 5 5
--------------------------------------------------------------------------------------------------------------
Val GTT 5 6 5 7 7 7 | Ala GCT 4 1 3 2 2 2 | Asp GAT 6 4 2 3 2 2 | Gly GGT 2 1 2 2 2 2
GTC 1 3 4 2 3 4 | GCC 2 2 1 2 4 4 | GAC 1 1 2 1 1 2 | GGC 2 2 2 2 2 1
GTA 2 1 1 1 1 2 | GCA 2 5 3 6 3 2 | Glu GAA 4 3 4 2 4 4 | GGA 3 3 3 2 1 1
GTG 2 1 2 0 2 3 | GCG 2 1 1 0 0 0 | GAG 1 3 1 0 1 1 | GGG 0 1 0 1 1 1
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
Phe TTT 4 4 4 4 6 5 | Ser TCT 0 0 0 0 1 0 | Tyr TAT 0 3 0 0 2 2 | Cys TGT 0 0 0 0 0 0
TTC 2 2 2 2 1 1 | TCC 0 3 1 1 0 1 | TAC 5 4 6 6 4 6 | TGC 0 0 0 0 0 0
Leu TTA 0 0 0 0 1 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
TTG 4 3 4 4 5 4 | TCG 1 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 4 4 4 4 4 4
--------------------------------------------------------------------------------------------------------------
Leu CTT 3 4 3 3 4 5 | Pro CCT 3 2 2 2 1 2 | His CAT 3 1 2 2 1 2 | Arg CGT 4 5 4 4 7 6
CTC 0 0 0 0 1 1 | CCC 3 1 1 1 1 1 | CAC 3 4 3 3 2 2 | CGC 2 3 3 3 1 1
CTA 1 0 0 0 0 0 | CCA 1 2 2 2 4 3 | Gln CAA 4 1 1 1 2 1 | CGA 2 1 1 1 1 1
CTG 2 3 4 4 2 1 | CCG 0 1 0 0 0 2 | CAG 4 2 6 6 4 3 | CGG 0 0 0 0 1 0
--------------------------------------------------------------------------------------------------------------
Ile ATT 6 6 3 3 1 5 | Thr ACT 1 3 1 1 2 3 | Asn AAT 1 3 4 4 2 1 | Ser AGT 1 1 1 1 2 0
ATC 4 4 4 4 6 5 | ACC 2 1 2 1 2 2 | AAC 2 3 4 5 5 1 | AGC 2 2 2 2 1 3
ATA 1 1 2 2 0 0 | ACA 1 1 0 0 0 0 | Lys AAA 2 3 3 3 2 2 | Arg AGA 4 5 4 4 6 5
Met ATG 4 6 5 5 2 4 | ACG 0 1 1 1 1 1 | AAG 5 7 5 5 2 6 | AGG 5 6 5 5 5 5
--------------------------------------------------------------------------------------------------------------
Val GTT 6 1 6 6 4 3 | Ala GCT 3 1 1 1 2 1 | Asp GAT 2 3 1 1 2 2 | Gly GGT 2 2 2 2 1 1
GTC 2 3 3 3 2 3 | GCC 5 3 3 4 4 5 | GAC 2 1 2 1 1 1 | GGC 1 1 1 1 4 1
GTA 2 0 1 1 3 2 | GCA 3 3 3 3 2 7 | Glu GAA 2 3 3 3 4 2 | GGA 1 2 2 2 2 2
GTG 2 0 1 1 3 2 | GCG 0 0 0 0 1 0 | GAG 1 2 2 2 0 1 | GGG 1 1 1 1 1 1
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------
Phe TTT 4 3 3 4 3 3 | Ser TCT 0 0 1 2 0 0 | Tyr TAT 1 3 2 0 2 2 | Cys TGT 0 0 0 0 0 0
TTC 0 1 1 1 1 1 | TCC 1 0 0 0 0 0 | TAC 5 4 4 6 7 7 | TGC 0 0 0 0 0 0
Leu TTA 0 0 2 0 1 1 | TCA 0 2 0 1 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
TTG 2 3 5 4 3 4 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 5 5 5 5 3 3
--------------------------------------------------------------------------------------------------------------
Leu CTT 2 4 4 4 3 3 | Pro CCT 1 1 1 1 1 1 | His CAT 2 1 2 1 1 2 | Arg CGT 6 4 6 6 5 4
CTC 1 0 1 0 0 0 | CCC 3 2 0 1 2 2 | CAC 1 1 1 2 2 0 | CGC 3 4 3 3 0 0
CTA 0 1 0 0 1 1 | CCA 4 1 4 3 2 2 | Gln CAA 0 1 1 3 3 4 | CGA 2 0 1 0 1 1
CTG 5 4 2 3 3 3 | CCG 0 0 2 0 1 1 | CAG 5 2 3 4 3 3 | CGG 0 1 2 0 0 0
--------------------------------------------------------------------------------------------------------------
Ile ATT 5 4 4 2 6 5 | Thr ACT 2 2 2 2 2 2 | Asn AAT 0 1 2 1 0 0 | Ser AGT 3 2 3 0 1 1
ATC 4 4 4 5 4 4 | ACC 0 1 2 2 2 1 | AAC 8 5 4 5 5 6 | AGC 1 2 1 3 1 1
ATA 2 2 1 1 2 2 | ACA 1 3 0 1 1 1 | Lys AAA 1 2 4 1 4 4 | Arg AGA 5 4 5 6 2 2
Met ATG 5 4 5 4 4 3 | ACG 1 2 2 1 1 1 | AAG 6 4 3 5 6 6 | AGG 3 4 2 4 2 3
--------------------------------------------------------------------------------------------------------------
Val GTT 2 4 4 5 5 6 | Ala GCT 3 2 3 2 4 4 | Asp GAT 1 2 1 3 4 4 | Gly GGT 2 4 2 1 2 2
GTC 2 1 1 2 1 1 | GCC 4 6 1 6 3 3 | GAC 1 1 3 1 1 1 | GGC 3 1 1 0 1 1
GTA 2 1 1 2 2 2 | GCA 4 7 6 4 1 1 | Glu GAA 3 3 2 3 3 3 | GGA 1 2 2 2 3 2
GTG 2 1 2 3 1 1 | GCG 0 1 0 0 0 0 | GAG 1 1 2 0 1 1 | GGG 0 1 1 2 1 2
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------
Phe TTT 2 | Ser TCT 1 | Tyr TAT 1 | Cys TGT 0
TTC 3 | TCC 0 | TAC 6 | TGC 0
Leu TTA 4 | TCA 1 | *** TAA 0 | *** TGA 0
TTG 3 | TCG 1 | TAG 0 | Trp TGG 4
--------------------------------------------------
Leu CTT 3 | Pro CCT 1 | His CAT 1 | Arg CGT 3
CTC 0 | CCC 1 | CAC 1 | CGC 4
CTA 0 | CCA 4 | Gln CAA 0 | CGA 2
CTG 3 | CCG 1 | CAG 4 | CGG 0
--------------------------------------------------
Ile ATT 4 | Thr ACT 3 | Asn AAT 4 | Ser AGT 2
ATC 2 | ACC 2 | AAC 1 | AGC 2
ATA 2 | ACA 1 | Lys AAA 6 | Arg AGA 5
Met ATG 5 | ACG 2 | AAG 5 | AGG 2
--------------------------------------------------
Val GTT 0 | Ala GCT 3 | Asp GAT 2 | Gly GGT 3
GTC 2 | GCC 3 | GAC 1 | GGC 2
GTA 2 | GCA 4 | Glu GAA 2 | GGA 1
GTG 0 | GCG 1 | GAG 0 | GGG 3
--------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: __1_H._rufescens
position 1: T:0.17910 C:0.18657 A:0.34328 G:0.29104
position 2: T:0.32090 C:0.15672 A:0.34328 G:0.17910
position 3: T:0.27612 C:0.23881 A:0.23134 G:0.25373
Average T:0.25871 C:0.19403 A:0.30597 G:0.24129
#2: __2_H._sorenseni
position 1: T:0.18657 C:0.20149 A:0.35075 G:0.26119
position 2: T:0.30597 C:0.17164 A:0.33582 G:0.18657
position 3: T:0.26119 C:0.24627 A:0.23134 G:0.26119
Average T:0.25124 C:0.20647 A:0.30597 G:0.23632
#3: __3_H._walallensis
position 1: T:0.18045 C:0.18045 A:0.35338 G:0.28571
position 2: T:0.30827 C:0.17293 A:0.32331 G:0.19549
position 3: T:0.25564 C:0.24812 A:0.24060 G:0.25564
Average T:0.24812 C:0.20050 A:0.30576 G:0.24561
#4: __4_H._kamtschatkana
position 1: T:0.18657 C:0.18657 A:0.35821 G:0.26866
position 2: T:0.31343 C:0.15672 A:0.32836 G:0.20149
position 3: T:0.26866 C:0.22388 A:0.22388 G:0.28358
Average T:0.25622 C:0.18905 A:0.30348 G:0.25124
#5: __5_H._sieboldii
position 1: T:0.15789 C:0.21053 A:0.34586 G:0.28571
position 2: T:0.31579 C:0.12782 A:0.36090 G:0.19549
position 3: T:0.28571 C:0.23308 A:0.23308 G:0.24812
Average T:0.25313 C:0.19048 A:0.31328 G:0.24311
#6: __6_H._discus_hannai
position 1: T:0.15789 C:0.19549 A:0.36090 G:0.28571
position 2: T:0.30075 C:0.15038 A:0.33835 G:0.21053
position 3: T:0.29323 C:0.22556 A:0.22556 G:0.25564
Average T:0.25063 C:0.19048 A:0.30827 G:0.25063
#7: __7_H._gigantea
position 1: T:0.15789 C:0.19549 A:0.35338 G:0.29323
position 2: T:0.30075 C:0.14286 A:0.34586 G:0.21053
position 3: T:0.29323 C:0.22556 A:0.22556 G:0.25564
Average T:0.25063 C:0.18797 A:0.30827 G:0.25313
#8: __8_H._corrugata
position 1: T:0.15789 C:0.22556 A:0.33083 G:0.28571
position 2: T:0.32331 C:0.15038 A:0.30827 G:0.21805
position 3: T:0.27068 C:0.24060 A:0.21805 G:0.27068
Average T:0.25063 C:0.20551 A:0.28571 G:0.25815
#9: __9_H._cracherodii
position 1: T:0.16418 C:0.23134 A:0.33582 G:0.26866
position 2: T:0.31343 C:0.12687 A:0.35821 G:0.20149
position 3: T:0.29851 C:0.23134 A:0.21642 G:0.25373
Average T:0.25871 C:0.19652 A:0.30348 G:0.24129
#10: _10_H._fulgens
position 1: T:0.18797 C:0.21053 A:0.35338 G:0.24812
position 2: T:0.30075 C:0.18045 A:0.30827 G:0.21053
position 3: T:0.27820 C:0.24060 A:0.23308 G:0.24812
Average T:0.25564 C:0.21053 A:0.29825 G:0.23559
#11: _11_H._roei
position 1: T:0.19084 C:0.24427 A:0.29008 G:0.27481
position 2: T:0.31298 C:0.15267 A:0.31298 G:0.22137
position 3: T:0.27481 C:0.28244 A:0.17557 G:0.26718
Average T:0.25954 C:0.22646 A:0.25954 G:0.25445
#12: _12_H._scalaris
position 1: T:0.16794 C:0.22901 A:0.31298 G:0.29008
position 2: T:0.32061 C:0.14504 A:0.30534 G:0.22901
position 3: T:0.26718 C:0.28244 A:0.18321 G:0.26718
Average T:0.25191 C:0.21883 A:0.26718 G:0.26209
#13: _13_H._laevigata
position 1: T:0.15267 C:0.26718 A:0.31298 G:0.26718
position 2: T:0.32824 C:0.17557 A:0.27481 G:0.22137
position 3: T:0.29771 C:0.26718 A:0.18321 G:0.25191
Average T:0.25954 C:0.23664 A:0.25700 G:0.24682
#14: _14_H._cyclobates
position 1: T:0.17424 C:0.22727 A:0.40152 G:0.19697
position 2: T:0.28030 C:0.16667 A:0.30303 G:0.25000
position 3: T:0.29545 C:0.26515 A:0.16667 G:0.27273
Average T:0.25000 C:0.21970 A:0.29040 G:0.23990
#15: _15_H._rubra
position 1: T:0.16031 C:0.24427 A:0.35115 G:0.24427
position 2: T:0.32061 C:0.12977 A:0.32061 G:0.22901
position 3: T:0.25954 C:0.28244 A:0.16794 G:0.29008
Average T:0.24682 C:0.21883 A:0.27990 G:0.25445
#16: _16_H._conicopora
position 1: T:0.16031 C:0.24427 A:0.35115 G:0.24427
position 2: T:0.32061 C:0.12977 A:0.32061 G:0.22901
position 3: T:0.25954 C:0.28244 A:0.16794 G:0.29008
Average T:0.24682 C:0.21883 A:0.27990 G:0.25445
#17: _17_H._pustulata
position 1: T:0.18321 C:0.24427 A:0.29771 G:0.27481
position 2: T:0.31298 C:0.16031 A:0.25191 G:0.27481
position 3: T:0.29008 C:0.26718 A:0.20611 G:0.23664
Average T:0.26209 C:0.22392 A:0.25191 G:0.26209
#18: _18_H._midae
position 1: T:0.17557 C:0.23664 A:0.32824 G:0.25954
position 2: T:0.31298 C:0.21374 A:0.24427 G:0.22901
position 3: T:0.29008 C:0.25954 A:0.19084 G:0.25954
Average T:0.25954 C:0.23664 A:0.25445 G:0.24936
#19: _19_H._ovina
position 1: T:0.13740 C:0.26718 A:0.35878 G:0.23664
position 2: T:0.29008 C:0.18321 A:0.26718 G:0.25954
position 3: T:0.25954 C:0.28244 A:0.19084 G:0.26718
Average T:0.22901 C:0.24427 A:0.27226 G:0.25445
#20: _20_H._diversicolor
position 1: T:0.15909 C:0.20455 A:0.34848 G:0.28788
position 2: T:0.28030 C:0.22727 A:0.23485 G:0.25758
position 3: T:0.28030 C:0.25000 A:0.21970 G:0.25000
Average T:0.23990 C:0.22727 A:0.26768 G:0.26515
#21: _21_H._varia
position 1: T:0.17424 C:0.25000 A:0.33333 G:0.24242
position 2: T:0.30303 C:0.18182 A:0.25758 G:0.25758
position 3: T:0.30303 C:0.20455 A:0.21970 G:0.27273
Average T:0.26010 C:0.21212 A:0.27020 G:0.25758
#22: _22_H._australis
position 1: T:0.17293 C:0.23308 A:0.32331 G:0.27068
position 2: T:0.30075 C:0.19549 A:0.26316 G:0.24060
position 3: T:0.25564 C:0.27820 A:0.20301 G:0.26316
Average T:0.24311 C:0.23559 A:0.26316 G:0.25815
#23: _23_H._t.tuberculata
position 1: T:0.16129 C:0.22581 A:0.34677 G:0.26613
position 2: T:0.32258 C:0.16129 A:0.33871 G:0.17742
position 3: T:0.31452 C:0.24194 A:0.20968 G:0.23387
Average T:0.26613 C:0.20968 A:0.29839 G:0.22581
#24: _24_H._t.coccinea
position 1: T:0.16935 C:0.21774 A:0.33871 G:0.27419
position 2: T:0.32258 C:0.15323 A:0.34677 G:0.17742
position 3: T:0.31452 C:0.22581 A:0.20968 G:0.25000
Average T:0.26882 C:0.19892 A:0.29839 G:0.23387
#25: _25_H._iris
position 1: T:0.19847 C:0.21374 A:0.36641 G:0.22137
position 2: T:0.26718 C:0.22137 A:0.25954 G:0.25191
position 3: T:0.25191 C:0.22901 A:0.25954 G:0.25954
Average T:0.23919 C:0.22137 A:0.29517 G:0.24427
Codon usage in genes
--------------------------------------------------------------
Phe TTT 39 48 | Ser TCT 0 10 | Tyr TAT 15 31 | Cys TGT 0 0
TTC 31 23 | TCC 0 10 | TAC 78 70 | TGC 0 0
Leu TTA 20 2 | TCA 0 7 | *** TAA 0 0 | *** TGA 0 0
TTG 53 16 | TCG 2 3 | TAG 0 0 | Trp TGG 65 37
--------------------------------------------------------------
Leu CTT 48 17 | Pro CCT 8 18 | His CAT 2 42 | Arg CGT 0 97
CTC 4 11 | CCC 1 27 | CAC 0 43 | CGC 0 60
CTA 2 2 | CCA 16 65 | Gln CAA 1 31 | CGA 1 21
CTG 80 16 | CCG 0 12 | CAG 24 71 | CGG 0 13
--------------------------------------------------------------
Ile ATT 52 44 | Thr ACT 1 42 | Asn AAT 30 44 | Ser AGT 0 20
ATC 91 3 | ACC 4 35 | AAC 13 80 | AGC 0 35
ATA 26 5 | ACA 2 16 | Lys AAA 0 78 | Arg AGA 18 120
Met ATG 100 29 | ACG 14 11 | AAG 26 111 | AGG 7 68
--------------------------------------------------------------
Val GTT 44 84 | Ala GCT 2 58 | Asp GAT 1 74 | Gly GGT 26 23
GTC 20 35 | GCC 0 73 | GAC 24 11 | GGC 24 17
GTA 15 22 | GCA 22 65 | Glu GAA 24 57 | GGA 34 17
GTG 5 26 | GCG 8 12 | GAG 0 26 | GGG 15 8
--------------------------------------------------------------
Codon position x base (3x4) table for each gene.
Gene #1
position 1: T:0.26626 C:0.16432 A:0.33743 G:0.23199
position 2: T:0.55360 C:0.07030 A:0.20914 G:0.16696
position 3: T:0.23550 C:0.25483 A:0.15905 G:0.35062
Average T:0.35179 C:0.16315 A:0.23521 G:0.24985
Gene #2
position 1: T:0.11942 C:0.25372 A:0.34433 G:0.28253
position 2: T:0.17797 C:0.21561 A:0.35734 G:0.24907
position 3: T:0.30297 C:0.24768 A:0.23606 G:0.21329
Average T:0.20012 C:0.23900 A:0.31258 G:0.24830
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 87 | Ser S TCT 10 | Tyr Y TAT 46 | Cys C TGT 0
TTC 54 | TCC 10 | TAC 148 | TGC 0
Leu L TTA 22 | TCA 7 | *** * TAA 0 | *** * TGA 0
TTG 69 | TCG 5 | TAG 0 | Trp W TGG 102
------------------------------------------------------------------------------
Leu L CTT 65 | Pro P CCT 26 | His H CAT 44 | Arg R CGT 97
CTC 15 | CCC 28 | CAC 43 | CGC 60
CTA 4 | CCA 81 | Gln Q CAA 32 | CGA 22
CTG 96 | CCG 12 | CAG 95 | CGG 13
------------------------------------------------------------------------------
Ile I ATT 96 | Thr T ACT 43 | Asn N AAT 74 | Ser S AGT 20
ATC 94 | ACC 39 | AAC 93 | AGC 35
ATA 31 | ACA 18 | Lys K AAA 78 | Arg R AGA 138
Met M ATG 129 | ACG 25 | AAG 137 | AGG 75
------------------------------------------------------------------------------
Val V GTT 128 | Ala A GCT 60 | Asp D GAT 75 | Gly G GGT 49
GTC 55 | GCC 73 | GAC 35 | GGC 41
GTA 37 | GCA 87 | Glu E GAA 81 | GGA 51
GTG 31 | GCG 20 | GAG 26 | GGG 23
------------------------------------------------------------------------------
(Ambiguity data are not used in the counts.)
Codon position x base (3x4) table, overall
position 1: T:0.17021 C:0.22280 A:0.34195 G:0.26505
position 2: T:0.30790 C:0.16535 A:0.30608 G:0.22067
position 3: T:0.27964 C:0.25015 A:0.20942 G:0.26079
Average T:0.25258 C:0.21277 A:0.28582 G:0.24883
Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)
__1_H._rufescens
__2_H._sorenseni 3.4195 (0.0581 0.0170)
__3_H._walallensis 4.7194 (0.0936 0.0198) 1.5215 (0.0563 0.0370)
__4_H._kamtschatkana 3.7286 (0.1078 0.0289) 2.4431 (0.0844 0.0346) 2.6160 (0.1290 0.0493)
__5_H._sieboldii 1.7428 (0.1222 0.0701) 1.4909 (0.1193 0.0800) 1.4940 (0.1321 0.0884) 1.5480 (0.1489 0.0962)
__6_H._discus_hannai 2.4504 (0.1803 0.0736) 1.9797 (0.1651 0.0834) 1.5555 (0.1526 0.0981) 2.3180 (0.2007 0.0866) 1.1844 (0.0565 0.0477)
__7_H._gigantea 2.6416 (0.1781 0.0674) 2.1103 (0.1631 0.0773) 1.6389 (0.1506 0.0919) 2.4708 (0.1985 0.0803) 1.3148 (0.0547 0.0416)-1.0000 (0.0064 0.0000)
__8_H._corrugata 1.3495 (0.1426 0.1056) 1.3523 (0.1332 0.0985) 1.4124 (0.1568 0.1110) 1.8378 (0.1773 0.0965) 2.0360 (0.1284 0.0630) 3.5019 (0.1762 0.0503) 3.9203 (0.1741 0.0444)
__9_H._cracherodii 1.9850 (0.2205 0.1111) 1.8431 (0.2111 0.1145) 1.7378 (0.2257 0.1299) 1.9105 (0.2642 0.1383) 2.8137 (0.1504 0.0535) 2.0571 (0.1728 0.0840) 2.2458 (0.1748 0.0778) 1.3398 (0.1329 0.0992)
_10_H._fulgens 1.1562 (0.2407 0.2082) 1.1907 (0.2458 0.2065) 1.0055 (0.2370 0.2357) 1.0681 (0.2367 0.2216) 1.6087 (0.2483 0.1544) 1.4175 (0.2395 0.1689) 1.3622 (0.2305 0.1692) 1.5551 (0.2328 0.1497) 1.5698 (0.2704 0.1722)
_11_H._roei 0.4688 (0.3509 0.7484) 0.4467 (0.3346 0.7490) 0.4292 (0.3422 0.7974) 0.5410 (0.3805 0.7032) 0.4423 (0.3061 0.6920) 0.4335 (0.3441 0.7937) 0.4505 (0.3439 0.7633) 0.3866 (0.3071 0.7943) 0.4791 (0.3415 0.7129) 0.4385 (0.3287 0.7496)
_12_H._scalaris 0.4611 (0.3841 0.8330) 0.4215 (0.3511 0.8330) 0.3933 (0.3524 0.8960) 0.5226 (0.4094 0.7835) 0.4108 (0.3205 0.7802) 0.4063 (0.3604 0.8869) 0.4222 (0.3602 0.8531) 0.3392 (0.2985 0.8801) 0.3931 (0.3378 0.8594) 0.5200 (0.4035 0.7760) 1.8859 (0.1194 0.0633)
_13_H._laevigata 0.4589 (0.3830 0.8346) 0.4194 (0.3500 0.8346) 0.3798 (0.3408 0.8973) 0.5272 (0.4141 0.7854) 0.3487 (0.3058 0.8768) 0.3753 (0.3562 0.9490) 0.3900 (0.3560 0.9127) 0.3593 (0.3244 0.9028) 0.4457 (0.3683 0.8262) 0.4776 (0.3779 0.7911) 1.5424 (0.1095 0.0710) 1.8705 (0.0935 0.0500)
_14_H._cyclobates 0.6729 (0.4542 0.6750) 0.6917 (0.4302 0.6219) 0.5795 (0.4333 0.7478) 0.7896 (0.5003 0.6335) 0.6439 (0.4412 0.6852) 0.6261 (0.4787 0.7646) 0.6591 (0.4846 0.7352) 0.6007 (0.4153 0.6914) 0.7570 (0.4669 0.6168) 0.6911 (0.4475 0.6475) 2.2092 (0.2333 0.1056) 2.0852 (0.2592 0.1243) 1.8398 (0.2431 0.1322)
_15_H._rubra 0.5483 (0.3858 0.7037) 0.5299 (0.3582 0.6760) 0.4534 (0.3438 0.7582) 0.6308 (0.4168 0.6608) 0.4783 (0.3312 0.6925) 0.4321 (0.3556 0.8231) 0.4491 (0.3554 0.7914) 0.4471 (0.3274 0.7323) 0.5774 (0.3828 0.6630) 0.6172 (0.4010 0.6496) 1.3592 (0.1194 0.0878) 1.6838 (0.1606 0.0954) 1.0141 (0.1337 0.1319) 1.6679 (0.1808 0.1084)
_16_H._conicopora 0.5483 (0.3858 0.7037) 0.5299 (0.3582 0.6760) 0.4534 (0.3438 0.7582) 0.6308 (0.4168 0.6608) 0.4783 (0.3312 0.6925) 0.4449 (0.3662 0.8231) 0.4624 (0.3660 0.7914) 0.4471 (0.3274 0.7323) 0.5611 (0.3720 0.6630) 0.6172 (0.4010 0.6496) 1.3592 (0.1194 0.0878) 1.6838 (0.1606 0.0954) 1.0141 (0.1337 0.1319) 1.6319 (0.1732 0.1061)-1.0000 (0.0065 0.0000)
_17_H._pustulata 0.5767 (0.4532 0.7859) 0.5513 (0.4084 0.7409) 0.4820 (0.4027 0.8354) 0.5691 (0.4475 0.7863) 0.4795 (0.3872 0.8073) 0.4940 (0.3895 0.7885) 0.5126 (0.3893 0.7594) 0.4543 (0.3562 0.7841) 0.5434 (0.4117 0.7576) 0.4726 (0.3755 0.7945) 0.3643 (0.1636 0.4491) 0.4887 (0.2067 0.4229) 0.5081 (0.2000 0.3935) 0.5688 (0.2656 0.4669) 0.3054 (0.1411 0.4622) 0.3140 (0.1451 0.4622)
_18_H._midae 0.4268 (0.3710 0.8692) 0.4297 (0.3515 0.8180) 0.3740 (0.3422 0.9150) 0.4280 (0.3961 0.9253) 0.4124 (0.3195 0.7747) 0.3563 (0.3240 0.9092) 0.3653 (0.3263 0.8932) 0.3089 (0.2787 0.9021) 0.3912 (0.2961 0.7571) 0.3423 (0.2801 0.8182) 0.6126 (0.1615 0.2636) 0.7585 (0.1993 0.2627) 0.6802 (0.1995 0.2932) 1.0695 (0.3000 0.2805) 0.7598 (0.2189 0.2881) 0.7598 (0.2189 0.2881) 0.4660 (0.2146 0.4606)
_19_H._ovina 0.5785 (0.4062 0.7021) 0.5532 (0.3686 0.6663) 0.4669 (0.3560 0.7625) 0.5247 (0.3760 0.7166) 0.6057 (0.3908 0.6452) 0.5129 (0.4025 0.7847) 0.5325 (0.4022 0.7554) 0.4737 (0.3458 0.7299) 0.7311 (0.4135 0.5655) 0.5271 (0.3518 0.6674) 0.6318 (0.1718 0.2720) 0.6535 (0.2130 0.3260) 0.6097 (0.1934 0.3171) 0.7482 (0.2279 0.3046) 0.5279 (0.1771 0.3355) 0.5279 (0.1771 0.3355) 0.4104 (0.1917 0.4672) 0.6510 (0.2647 0.4066)
_20_H._diversicolor 0.3931 (0.3500 0.8904) 0.3886 (0.3260 0.8388) 0.3716 (0.3364 0.9054) 0.4162 (0.3636 0.8735) 0.4809 (0.3827 0.7957) 0.4484 (0.3750 0.8363) 0.4786 (0.3857 0.8058) 0.4040 (0.3403 0.8423) 0.5117 (0.4170 0.8148) 0.5416 (0.3890 0.7181) 0.6281 (0.2042 0.3252) 0.6238 (0.2287 0.3666) 0.6009 (0.2323 0.3866) 1.0485 (0.3347 0.3192) 0.8982 (0.2736 0.3046) 0.9296 (0.2832 0.3046) 0.4246 (0.2469 0.5815) 0.3835 (0.2123 0.5534) 0.5408 (0.1886 0.3488)
_21_H._varia 0.5062 (0.4048 0.7995) 0.4615 (0.3666 0.7945) 0.4295 (0.3518 0.8192) 0.4682 (0.3848 0.8219) 0.5212 (0.3841 0.7369) 0.4260 (0.3836 0.9005) 0.4423 (0.3834 0.8668) 0.3999 (0.3299 0.8249) 0.5554 (0.4059 0.7309) 0.4937 (0.3495 0.7080) 0.4582 (0.2035 0.4441) 0.4871 (0.2504 0.5141) 0.4873 (0.2565 0.5265) 0.5532 (0.3278 0.5925) 0.4498 (0.2452 0.5452) 0.4332 (0.2362 0.5452) 0.4019 (0.2164 0.5384) 0.5142 (0.2537 0.4933) 0.4742 (0.1379 0.2907) 0.3222 (0.1843 0.5720)
_22_H._australis 0.5454 (0.3717 0.6816) 0.4901 (0.3346 0.6826) 0.4320 (0.3122 0.7227) 0.5713 (0.3765 0.6590) 0.5356 (0.3292 0.6147) 0.4704 (0.3208 0.6820) 0.5035 (0.3306 0.6565) 0.5174 (0.3283 0.6346) 0.6297 (0.3621 0.5751) 0.5628 (0.3396 0.6035) 0.4530 (0.1468 0.3241) 0.5904 (0.1887 0.3196) 0.4921 (0.1641 0.3334) 0.7647 (0.2746 0.3590) 0.5758 (0.1877 0.3260) 0.6018 (0.1962 0.3260) 0.5015 (0.2078 0.4143) 0.5357 (0.2124 0.3964) 0.4351 (0.1846 0.4243) 0.3055 (0.1500 0.4909) 0.3666 (0.2198 0.5995)
_23_H._t.tuberculata 0.5584 (0.3912 0.7005) 0.6095 (0.4000 0.6563) 0.5653 (0.4011 0.7095) 0.5927 (0.4432 0.7477) 0.5870 (0.4014 0.6838) 0.6151 (0.4240 0.6894) 0.6222 (0.4207 0.6762) 0.5437 (0.3795 0.6981) 0.6450 (0.4058 0.6291) 0.4934 (0.4093 0.8294) 0.7112 (0.2270 0.3192) 0.7660 (0.2757 0.3599) 0.8320 (0.2698 0.3243) 0.7634 (0.2768 0.3626) 0.5316 (0.2095 0.3942) 0.5134 (0.2041 0.3976) 0.8275 (0.1866 0.2255) 0.7358 (0.2760 0.3752) 0.8350 (0.2854 0.3418) 0.5825 (0.3309 0.5681) 0.5974 (0.3142 0.5260) 0.7356 (0.2746 0.3732)
_24_H._t.coccinea 0.5400 (0.3835 0.7101) 0.6070 (0.3951 0.6510) 0.5012 (0.3846 0.7674) 0.6445 (0.4381 0.6796) 0.5761 (0.3908 0.6783) 0.6312 (0.4130 0.6544) 0.6385 (0.4098 0.6417) 0.6078 (0.3777 0.6214) 0.6119 (0.4004 0.6544) 0.4730 (0.4094 0.8655) 0.6865 (0.2319 0.3378) 0.7537 (0.2860 0.3794) 0.7873 (0.2698 0.3427) 0.6993 (0.2819 0.4032) 0.5276 (0.2189 0.4149) 0.5100 (0.2134 0.4185) 0.8896 (0.1935 0.2176) 0.7640 (0.2864 0.3749) 0.8654 (0.3039 0.3511) 0.6412 (0.3561 0.5554) 0.6486 (0.3333 0.5138) 0.6456 (0.2797 0.4332) 1.3231 (0.0319 0.0241)
_25_H._iris 0.9376 (0.4857 0.5180) 0.8452 (0.4552 0.5386) 0.9136 (0.4591 0.5025) 0.8482 (0.4745 0.5594) 1.0104 (0.4652 0.4604) 1.0001 (0.4930 0.4929) 1.0262 (0.4959 0.4832) 0.8870 (0.4466 0.5035) 0.9604 (0.4982 0.5188) 0.7013 (0.4302 0.6134) 0.6136 (0.3024 0.4927) 0.6247 (0.3446 0.5517) 0.6046 (0.3413 0.5645) 0.7647 (0.3761 0.4918) 0.7035 (0.3287 0.4673) 0.6817 (0.3185 0.4673) 0.4765 (0.3332 0.6992) 0.3764 (0.2941 0.7814) 0.3831 (0.2558 0.6677) 0.3292 (0.2647 0.8043) 0.3849 (0.2932 0.7616) 0.4867 (0.3067 0.6301) 0.7794 (0.3927 0.5039) 0.7453 (0.4018 0.5390)
TREE # 1: ((10, (((4, (1, (2, 3))), (5, (6, 7))), (8, 9))), 25, ((17, (24, 23)), (22, ((18, ((11, (12, 13)), (14, (15, 16)))), ((19, 21), 20))))); MP score: -1
lnL(ntime: 47 np: 50): -4549.994728 +0.000000
26..27 27..10 27..28 28..29 29..30 30..4 30..31 31..1 31..32 32..2 32..3 29..33 33..5 33..34 34..6 34..7 28..35 35..8 35..9 26..25 26..36 36..37 37..17 37..38 38..24 38..23 36..39 39..22 39..40 40..41 41..18 41..42 42..43 43..11 43..44 44..12 44..13 42..45 45..14 45..46 46..15 46..16 40..47 47..48 48..19 48..21 47..20
0.268952 0.171730 0.083766 0.035518 0.074410 0.083434 0.011002 0.045450 0.010919 0.012703 0.061348 0.047496 0.010039 0.063343 0.007043 0.000004 0.022222 0.054010 0.133771 0.326804 0.080408 0.119873 0.106308 0.173673 0.030787 0.012884 0.028726 0.142284 0.019369 0.048245 0.214417 0.039258 0.012747 0.043022 0.061997 0.067735 0.052575 0.071543 0.189012 0.050850 0.006571 0.000589 0.059272 0.073497 0.089902 0.167361 0.181324 2.755510 1.546344 0.946822
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 3.66819 (1st gene)
((10: 0.171730, (((4: 0.083434, (1: 0.045450, (2: 0.012703, 3: 0.061348): 0.010919): 0.011002): 0.074410, (5: 0.010039, (6: 0.007043, 7: 0.000004): 0.063343): 0.047496): 0.035518, (8: 0.054010, 9: 0.133771): 0.022222): 0.083766): 0.268952, 25: 0.326804, ((17: 0.106308, (24: 0.030787, 23: 0.012884): 0.173673): 0.119873, (22: 0.142284, ((18: 0.214417, ((11: 0.043022, (12: 0.067735, 13: 0.052575): 0.061997): 0.012747, (14: 0.189012, (15: 0.006571, 16: 0.000589): 0.050850): 0.071543): 0.039258): 0.048245, ((19: 0.089902, 21: 0.167361): 0.073497, 20: 0.181324): 0.059272): 0.019369): 0.028726): 0.080408);
((_10_H._fulgens: 0.171730, (((__4_H._kamtschatkana: 0.083434, (__1_H._rufescens: 0.045450, (__2_H._sorenseni: 0.012703, __3_H._walallensis: 0.061348): 0.010919): 0.011002): 0.074410, (__5_H._sieboldii: 0.010039, (__6_H._discus_hannai: 0.007043, __7_H._gigantea: 0.000004): 0.063343): 0.047496): 0.035518, (__8_H._corrugata: 0.054010, __9_H._cracherodii: 0.133771): 0.022222): 0.083766): 0.268952, _25_H._iris: 0.326804, ((_17_H._pustulata: 0.106308, (_24_H._t.coccinea: 0.030787, _23_H._t.tuberculata: 0.012884): 0.173673): 0.119873, (_22_H._australis: 0.142284, ((_18_H._midae: 0.214417, ((_11_H._roei: 0.043022, (_12_H._scalaris: 0.067735, _13_H._laevigata: 0.052575): 0.061997): 0.012747, (_14_H._cyclobates: 0.189012, (_15_H._rubra: 0.006571, _16_H._conicopora: 0.000589): 0.050850): 0.071543): 0.039258): 0.048245, ((_19_H._ovina: 0.089902, _21_H._varia: 0.167361): 0.073497, _20_H._diversicolor: 0.181324): 0.059272): 0.019369): 0.028726): 0.080408);
Detailed output identifying parameters
rates for 2 genes: 1 2.75551
kappa (ts/tv) = 1.54634
omega (dN/dS) = 0.94682
Time used: 2:21
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