YN00 examples/abglobin.nuc
ns = 5 ls = 285
Codon position x base (3x4) table for each sequence.
human
position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649
position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333
position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140
goat-cow
position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000
position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035
position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088
rabbit
position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140
position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684
position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439
rat
position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895
position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439
position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421
marsupial
position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439
position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333
position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123
Average
position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825
position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965
position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842
Codon usage for each species
--------------------------------------------------------------------------------------------------
Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2
TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3
Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0
TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4
--------------------------------------------------------------------------------------------------
Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1
CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0
CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0
CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0
--------------------------------------------------------------------------------------------------
Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1
ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3
ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2
Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2
--------------------------------------------------------------------------------------------------
Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10
GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5
GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3
GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2
--------------------------------------------------------------------------------------------------
Sums
--------------------------------------------------
Phe TTT 25 | Ser TCT 25 | Tyr TAT 10 | Cys TGT 8
TTC 51 | TCC 31 | TAC 19 | TGC 9
Leu TTA 0 | TCA 1 | *** TAA 0 | *** TGA 0
TTG 12 | TCG 3 | TAG 0 | Trp TGG 16
--------------------------------------------------
Leu CTT 6 | Pro CCT 23 | His CAT 21 | Arg CGT 7
CTC 24 | CCC 25 | CAC 68 | CGC 1
CTA 6 | CCA 3 | Gln CAA 1 | CGA 0
CTG 123 | CCG 5 | CAG 25 | CGG 2
--------------------------------------------------
Ile ATT 6 | Thr ACT 24 | Asn AAT 16 | Ser AGT 13
ATC 12 | ACC 53 | AAC 35 | AGC 19
ATA 1 | ACA 2 | Lys AAA 20 | Arg AGA 3
Met ATG 17 | ACG 0 | AAG 98 | AGG 17
--------------------------------------------------
Val GTT 24 | Ala GCT 50 | Asp GAT 31 | Gly GGT 30
GTC 19 | GCC 92 | GAC 48 | GGC 60
GTA 2 | GCA 7 | Glu GAA 19 | GGA 7
GTG 89 | GCG 14 | GAG 40 | GGG 7
--------------------------------------------------
Nei & Gojobori 1986. dN/dS (dN, dS)
human
goat-cow 0.251(0.0863 0.3443)
rabbit 0.263(0.0867 0.3301) 0.294(0.1054 0.3581)
rat 0.204(0.1261 0.6164) 0.246(0.1493 0.6065) 0.218(0.1348 0.6187)
marsupial 0.190(0.1931 1.0148) 0.189(0.1910 1.0099) 0.218(0.2111 0.9668) 0.272(0.2404 0.8852)
Estimation by the method of Yang & Nielsen (2000):
(equal weighting of pathways)
seq. seq. S N t kappa omega dN +- SE dS +- SE
2 1 183.7 671.3 0.5169 1.5804 0.1625 0.0818 +- 0.0115 0.5031 +- 0.0930
3 1 177.5 677.5 0.5033 1.5804 0.1642 0.0815 +- 0.0114 0.4967 +- 0.0927
3 2 180.1 674.9 0.5627 1.5804 0.1929 0.0997 +- 0.0128 0.5169 +- 0.0925
4 1 191.3 663.7 0.9075 1.5804 0.1308 0.1216 +- 0.0144 0.9301 +- 0.1987
4 2 192.4 662.6 0.9642 1.5804 0.1557 0.1447 +- 0.0159 0.9297 +- 0.2091
4 3 187.0 668.0 0.9790 1.5804 0.1262 0.1298 +- 0.0149 1.0286 +- 0.2614
5 1 189.3 665.7 2.1638 1.5804 0.0711 0.1853 +- 0.0184 2.6055 +- 3.9344
5 2 190.4 664.6 1.2984 1.5804 0.1416 0.1842 +- 0.0184 1.3008 +- 0.1995
5 3 185.2 669.8 1.3214 1.5804 0.1554 0.2023 +- 0.0194 1.3020 +- 0.2026
5 4 194.5 660.5 1.5554 1.5804 0.1591 0.2354 +- 0.0215 1.4797 +- 0.5173