| blob | 829927ac7cb5f78e6e5a74f5d6077e2a9a2c07a6 |
2 seed used = 162469585
4 Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAC AAC ACA CGA GCT ACA AAC TAC AAT GCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AGT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT GTC CGT CAG TAT GTT CAA GGT TGT GGA GTG
5 Hla_gibbon AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA CGA GCT ACA AAC TAC AAT CCT GGA GAC AGA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT GAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT TTA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCC GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CGT TGT CAA AAC AGA GAT CTC CGT CAG TAT ATT CAA GGT TGT GGA GTA
6 Cgu/Can_colobus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAC GCT ACA AAC TAC AAT CCT GGA GAT GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA AAT AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT CGA GCA TGG GTG GCA TGG AAA AAG CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT GAA GGT TGT GGA GTA
7 Pne_langur AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AAA TTG GGA CTG GAT GGC TAC AAG GGA GTC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT GGT TAT AAC ACA GAA GCT ACA AAC TAC AAT CCT GGA GAC GAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CGC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT GAT GCC TGT CAT ATA TCC TGC AGT GCT TTG CTG CAA AAC AAC ATC GCT GAT GCT GTA GCT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC GTT CGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AAA GAT GTC AGT CAG TAC GTT AAA GGT TGT GGA GTG
8 Mmu_rhesus AAG ATC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG GTG TGT TTG GCC AAA TGG GAG AGT AAT TAT AAC ACA CAA GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAC TGG TGT AAT AAT GGC AAA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT AAC ATC GCT GAT GCT GTA ACT TGT GCA AAG AGG GTT GTC AGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AGA AAT CAC TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTG
9 Ssc_squirrelM AAG GTC TTC GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG CTT GGA ATG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAC TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAT AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT CAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGT GAT CCA CAA GGC ATT AGA GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA
10 Cja_marmoset AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGG TTT GGA CTG GAT GGC TAC AGG GGA ATC AGC CTA GCA AAC TGG ATG TGT TTG GCC AAA TGG GAG AGT GAT TAT AAC ACA CGT GCT ACA AAC TAC AAT CCT GGA GAC CAA AGC ACT GAT TAT GGG ATA TTT CAG ATC AAT AGC CAC TAT TGG TGT AAC AAT GGC AGA ACC CCA GGA GCA GTT AAT GCC TGT CAT ATA TCC TGC AAT GCT TTG CTG CAA GAT GAC ATC ACT GAA GCT GTG GCC TGT GCA AAG AGG GTT GTC CGC GAT CCA CAA GGC ATT AGG GCA TGG GTG GCA TGG AAA GCT CAT TGT CAA AAC AGA GAT GTC AGT CAG TAT GTT CAA GGT TGT GGA GTA
13 CODONML (in paml 3.14, January 2004) lysozymeSmall.txt Model: several dN/dS ratios for branches
14 Codon frequencies: F3x4
16 ns = 7 ls = 130
17 # site patterns = 81
18 2 1 1 1 2 7 2 3 3 1 2 2 2 1 1
19 5 1 4 3 2 1 1 3 1 5 4 5 1 1 1
20 1 2 1 3 2 1 1 1 1 1 1 1 2 2 1
21 1 1 1 1 1 2 2 1 1 1 1 1 1 3 1
22 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
23 1 1 1 1 1 1
25 1
26 Hsa_Human AAG GTC TTT GAA AGG TGT GAG TTG GCC AGA ACT CTG AAA AGA TTG GGA ATG GAT GGC TAC AGG ATC AGC CTA GCA AAC TGG ATG AGT GGT TAC ACA CGA GCT AAT GCT GAC AGA TAT GGG ATA TTT CAG ATC CGC TAC AAT GAT AAA ACC CCA GTT AAT CAT TTA TCC TGC AGT CAA GAT AAC GCT GAT GTA GCT GTC CGT ATT AGA GTG AGA AAT CGT AGA GTC CGT TAT GTT CAA GGT GTG
27 Hla_gibbon ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ..C ... ... ... ... ..C ... ... ... ... ... ... ... C.. ... ... A.. ... ... ..A
28 Cgu/Can_colobus ... A.. ... ... ... ... ... ... ... ... ... ... ... .A. ... ... C.. ... ... ... .A. G.. ... ... ... ... ... G.. ... ... ..T ... GAC ... ... C.. ..T GA. ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... A.. ... ... ... ... ... ... A.. ... C.. ... .A. ..G .AC ... ... A.. ... ... G.. ... ..A
29 Pne_langur ... A.. ... ... ... ... ... ... ... ... ... ... ... .A. ... ... C.. ... ... ... .A. G.. ... ... ... ... ... G.. ... ... ..T ... GA. ... ... C.. ... GA. ... ... ... ... ... ... ... ... ... A.. ... ... ... ... G.. ... A.. ... ... ... ... A.C ... ... ... ... ... ... A.. G.. C.. ... ... ... .AC .A. ... A.. ..C ... A.. ... ...
30 Mmu_rhesus ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... G.. ... AA. ..T ... .A. ... ... C.. ... CA. ... ... ... ... ... ... .A. ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... ... ... ... ... ... A.. ... A.. ... ... ... ... ... .AC ... ... A.. ... ... ... ... ...
31 Ssc_squirrelM ... ... ..C ... ... ... ... ... ... ... ... ... ... ..G C.T ... ... ... ... ... ... ... ... ... ... ... ... ... ... .AC ..T ... ..T ... ... C.. ... CA. ... ... ... ... ... ... .A. ..T ... A.. .G. ... ... ... ... ... A.. ... ... .A. ... ... G.. A.. C.A ..G ..C ... ... ... ... ... .A. GC. .A. ... ... A.. ... ... ... ... ..A
32 Cja_marmoset ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ..T ... C.. ... ... ... ... ... ... ... ... ... ... ... ... .A. ..T ... ..T ... ... C.. ... CA. ... ... ... ... ... ... .A. ..T ..C A.. .G. ... ... ... ... ... A.. ... ... .A. ... ... G.. A.. ..A ..G ..C ... ..C ... ..G ... .A. GC. .A. ... ... A.. ... ... ... ... ..A
34 Codon usage in sequences
35 --------------------------------------------------------------------------------------------------------------
36 Phe TTT 2 2 2 2 2 1 | Ser TCT 0 0 0 0 0 0 | Tyr TAT 2 3 3 2 3 4 | Cys TGT 7 7 7 7 7 7
37 TTC 0 0 0 0 0 1 | TCC 1 1 1 1 1 1 | TAC 4 3 3 4 3 2 | TGC 1 1 1 1 1 1
38 Leu TTA 1 1 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
39 TTG 4 4 4 4 4 3 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 5 5 5 5 5 5
40 --------------------------------------------------------------------------------------------------------------
41 Leu CTT 0 0 0 0 0 1 | Pro CCT 0 1 1 1 1 1 | His CAT 1 1 1 1 1 2 | Arg CGT 3 2 0 0 0 2
42 CTC 0 1 0 0 0 0 | CCC 0 0 0 0 0 0 | CAC 0 0 1 1 2 1 | CGC 1 2 1 1 0 0
43 CTA 1 1 1 1 1 1 | CCA 2 2 2 2 2 2 | Gln CAA 4 4 3 3 6 6 | CGA 1 1 1 1 0 0
44 CTG 2 2 3 3 3 2 | CCG 0 0 0 0 0 0 | CAG 2 2 2 2 2 2 | CGG 0 0 0 0 0 0
45 --------------------------------------------------------------------------------------------------------------
46 Ile ATT 1 2 1 0 1 1 | Thr ACT 2 2 2 2 3 3 | Asn AAT 5 6 7 5 8 6 | Ser AGT 2 1 3 4 3 2
47 ATC 3 3 3 3 4 3 | ACC 1 1 1 1 1 1 | AAC 5 5 5 6 5 4 | AGC 3 3 3 3 3 3
48 ATA 1 1 2 2 2 2 | ACA 2 2 2 2 2 2 | Lys AAA 3 3 5 6 3 3 | Arg AGA 6 6 2 2 5 4
49 Met ATG 2 2 0 0 0 2 | ACG 0 0 0 0 0 0 | AAG 2 2 4 3 2 2 | AGG 3 3 2 2 3 4
50 --------------------------------------------------------------------------------------------------------------
51 Val GTT 3 2 3 4 3 3 | Ala GCT 6 4 5 5 4 4 | Asp GAT 7 7 6 6 6 5 | Gly GGT 2 2 2 2 1 1
52 GTC 3 2 3 3 2 3 | GCC 3 4 3 3 3 4 | GAC 1 1 1 1 1 3 | GGC 3 3 3 3 3 3
53 GTA 1 2 2 1 1 1 | GCA 5 5 5 5 5 5 | Glu GAA 1 1 3 3 1 1 | GGA 5 5 5 5 5 5
54 GTG 2 1 2 3 3 2 | GCG 0 0 0 0 0 0 | GAG 2 2 2 2 2 2 | GGG 1 1 1 1 1 1
55 --------------------------------------------------------------------------------------------------------------
57 --------------------------------------------------
58 Phe TTT 3 | Ser TCT 0 | Tyr TAT 4 | Cys TGT 7
59 TTC 0 | TCC 1 | TAC 2 | TGC 1
60 Leu TTA 0 | TCA 0 | *** TAA 0 | *** TGA 0
61 TTG 3 | TCG 0 | TAG 0 | Trp TGG 5
62 --------------------------------------------------
63 Leu CTT 0 | Pro CCT 1 | His CAT 2 | Arg CGT 1
64 CTC 0 | CCC 0 | CAC 1 | CGC 1
65 CTA 1 | CCA 2 | Gln CAA 5 | CGA 0
66 CTG 3 | CCG 0 | CAG 2 | CGG 0
67 --------------------------------------------------
68 Ile ATT 1 | Thr ACT 3 | Asn AAT 5 | Ser AGT 2
69 ATC 3 | ACC 1 | AAC 5 | AGC 3
70 ATA 2 | ACA 2 | Lys AAA 3 | Arg AGA 3
71 Met ATG 1 | ACG 0 | AAG 2 | AGG 5
72 --------------------------------------------------
73 Val GTT 3 | Ala GCT 4 | Asp GAT 6 | Gly GGT 1
74 GTC 3 | GCC 4 | GAC 2 | GGC 3
75 GTA 1 | GCA 5 | Glu GAA 2 | GGA 5
76 GTG 2 | GCG 0 | GAG 2 | GGG 1
77 --------------------------------------------------
79 Codon position x base (3x4) table for each sequence.
81 #1: Hsa_Human
82 position 1: T:0.20769 C:0.13077 A:0.31538 G:0.34615
83 position 2: T:0.20000 C:0.16923 A:0.30000 G:0.33077
84 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231
86 #2: Hla_gibbon
87 position 1: T:0.20769 C:0.14615 A:0.32308 G:0.32308
88 position 2: T:0.20000 C:0.16923 A:0.30769 G:0.32308
89 position 3: T:0.32308 C:0.23077 A:0.26154 G:0.18462
91 #3: Cgu/Can_colobus
92 position 1: T:0.20000 C:0.12308 A:0.32308 G:0.35385
93 position 2: T:0.20000 C:0.16923 A:0.35385 G:0.27692
94 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231
96 #4: Pne_langur
97 position 1: T:0.20000 C:0.12308 A:0.31538 G:0.36154
98 position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462
99 position 3: T:0.31538 C:0.23846 A:0.25385 G:0.19231
101 #5: Mmu_rhesus
102 position 1: T:0.20000 C:0.13846 A:0.34615 G:0.31538
103 position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462
104 position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231
106 #6: Ssc_squirrelM
107 position 1: T:0.19231 C:0.15385 A:0.32308 G:0.33077
108 position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231
109 position 3: T:0.33077 C:0.23077 A:0.24615 G:0.19231
111 #7: Cja_marmoset
112 position 1: T:0.20000 C:0.14615 A:0.31538 G:0.33846
113 position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231
114 position 3: T:0.33077 C:0.23077 A:0.23846 G:0.20000
116 Sums of codon usage counts
117 ------------------------------------------------------------------------------
118 Phe F TTT 14 | Ser S TCT 0 | Tyr Y TAT 21 | Cys C TGT 49
119 TTC 1 | TCC 7 | TAC 21 | TGC 7
120 Leu L TTA 2 | TCA 0 | *** * TAA 0 | *** * TGA 0
121 TTG 26 | TCG 0 | TAG 0 | Trp W TGG 35
122 ------------------------------------------------------------------------------
123 Leu L CTT 1 | Pro P CCT 6 | His H CAT 9 | Arg R CGT 8
124 CTC 1 | CCC 0 | CAC 6 | CGC 6
125 CTA 7 | CCA 14 | Gln Q CAA 31 | CGA 4
126 CTG 18 | CCG 0 | CAG 14 | CGG 0
127 ------------------------------------------------------------------------------
128 Ile I ATT 7 | Thr T ACT 17 | Asn N AAT 42 | Ser S AGT 17
129 ATC 22 | ACC 7 | AAC 35 | AGC 21
130 ATA 12 | ACA 14 | Lys K AAA 26 | Arg R AGA 28
131 Met M ATG 7 | ACG 0 | AAG 17 | AGG 22
132 ------------------------------------------------------------------------------
133 Val V GTT 21 | Ala A GCT 32 | Asp D GAT 43 | Gly G GGT 11
134 GTC 19 | GCC 24 | GAC 10 | GGC 21
135 GTA 9 | GCA 35 | Glu E GAA 12 | GGA 35
136 GTG 15 | GCG 0 | GAG 14 | GGG 7
137 ------------------------------------------------------------------------------
140 Codon position x base (3x4) table, overall
142 position 1: T:0.20110 C:0.13736 A:0.32308 G:0.33846
143 position 2: T:0.20000 C:0.17143 A:0.33077 G:0.29780
144 position 3: T:0.32747 C:0.22857 A:0.25165 G:0.19231
146 Codon frequencies under model, for use in evolver:
147 0.01378574 0.00962226 0.01059374 0.00809565
148 0.01181635 0.00824765 0.00908035 0.00693913
149 0.02279949 0.01591374 0.00000000 0.00000000
150 0.02052711 0.01432765 0.00000000 0.01205451
151 0.00941649 0.00657258 0.00723616 0.00552982
152 0.00807127 0.00563364 0.00620242 0.00473984
153 0.01557342 0.01087004 0.01196749 0.00914546
154 0.01402125 0.00978665 0.01077472 0.00823396
155 0.02214758 0.01545871 0.01701945 0.01300613
156 0.01898364 0.01325032 0.01458810 0.01114811
157 0.03662868 0.02556633 0.02814755 0.02151013
158 0.03297798 0.02301819 0.02534214 0.01936627
159 0.02320222 0.01619484 0.01782990 0.01362547
160 0.01988762 0.01388129 0.01528277 0.01167897
161 0.03837291 0.02678377 0.02948791 0.02253443
162 0.03454836 0.02411429 0.02654891 0.02028847
166 Nei & Gojobori 1986. dN/dS (dN, dS)
167 (Note: This matrix is not used in later m.l. analysis.
168 Use runmode = -2 for ML pairwise comparison.)
170 Hsa_Human
171 Hla_gibbon 0.2782 (0.0133 0.0478)
172 Cgu/Can_colobus 1.1086 (0.0742 0.0670) 1.1055 (0.0742 0.0671)
173 Pne_langur 1.1979 (0.0725 0.0605) 0.9234 (0.0797 0.0863) 0.5517 (0.0267 0.0484)
174 Mmu_rhesus 1.8744 (0.0562 0.0300) 1.0215 (0.0561 0.0550) 1.2973 (0.0473 0.0364) 1.3970 (0.0508 0.0364)
175 Ssc_squirrelM 0.4701 (0.0633 0.1346) 0.4688 (0.0633 0.1349) 0.5159 (0.0775 0.1502) 0.5833 (0.0959 0.1645) 0.4544 (0.0559 0.1230)
176 Cja_marmoset 0.4725 (0.0634 0.1341) 0.5925 (0.0633 0.1069) 0.4702 (0.0704 0.1496) 0.5411 (0.0886 0.1638) 0.3995 (0.0490 0.1225) 0.1595 (0.0099 0.0619)
179 TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65
180 lnL(ntime: 11 np: 14): -904.636553 +0.000000
181 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7
182 0.07000 0.02557 0.03893 0.04388 0.07904 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56118 0.68580 3.50575
183 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
185 tree length = 0.55906
187 ((1: 0.025570, 2: 0.038929): 0.070000, ((3: 0.043878, 4: 0.052151): 0.079045, 5: 0.019487): 0.043879, (6: 0.041033, 7: 0.023779): 0.121307);
189 ((Hsa_Human: 0.025570, Hla_gibbon: 0.038929): 0.070000, ((Cgu/Can_colobus: 0.043878, Pne_langur: 0.052151): 0.079045, Mmu_rhesus: 0.019487): 0.043879, (Ssc_squirrelM: 0.041033, Cja_marmoset: 0.023779): 0.121307);
191 Detailed output identifying parameters
193 kappa (ts/tv) = 4.56118
195 dN & dS for each branch
197 branch t S N dN/dS dN dS S*dS N*dN
199 8..9 0.070 107.8 282.2 0.6858 0.0207 0.0302 3.3 5.8
200 9..1 0.026 107.8 282.2 0.6858 0.0076 0.0110 1.2 2.1
201 9..2 0.039 107.8 282.2 0.6858 0.0115 0.0168 1.8 3.2
202 8..10 0.044 107.8 282.2 0.6858 0.0130 0.0189 2.0 3.7
203 10..11 0.079 107.8 282.2 3.5057 0.0328 0.0094 1.0 9.3
204 11..3 0.044 107.8 282.2 0.6858 0.0130 0.0189 2.0 3.7
205 11..4 0.052 107.8 282.2 0.6858 0.0154 0.0225 2.4 4.4
206 10..5 0.019 107.8 282.2 0.6858 0.0058 0.0084 0.9 1.6
207 8..12 0.121 107.8 282.2 0.6858 0.0359 0.0523 5.6 10.1
208 12..6 0.041 107.8 282.2 0.6858 0.0121 0.0177 1.9 3.4
209 12..7 0.024 107.8 282.2 0.6858 0.0070 0.0103 1.1 2.0
211 tree length for dN: 0.17485
212 tree length for dS: 0.21644
214 dS tree:
215 ((Hsa_Human: 0.011031, Hla_gibbon: 0.016794): 0.030198, ((Cgu/Can_colobus: 0.018929, Pne_langur: 0.022498): 0.009367, Mmu_rhesus: 0.008407): 0.018929, (Ssc_squirrelM: 0.017702, Cja_marmoset: 0.010258): 0.052332);
216 dN tree:
217 ((Hsa_Human: 0.007565, Hla_gibbon: 0.011517): 0.020710, ((Cgu/Can_colobus: 0.012982, Pne_langur: 0.015429): 0.032838, Mmu_rhesus: 0.005765): 0.012982, (Ssc_squirrelM: 0.012140, Cja_marmoset: 0.007035): 0.035889);
221 TREE # 2: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65
222 lnL(ntime: 11 np: 14): -904.636553 -0.000000
223 8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7
224 0.07000 0.02557 0.03893 0.04388 0.07905 0.04388 0.05215 0.01949 0.12131 0.04103 0.02378 4.56122 0.68581 3.50574
225 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
227 tree length = 0.55906
229 ((1: 0.025570, 2: 0.038929): 0.070001, ((3: 0.043878, 4: 0.052150): 0.079045, 5: 0.019488): 0.043879, (6: 0.041033, 7: 0.023779): 0.121307);
231 ((Hsa_Human: 0.025570, Hla_gibbon: 0.038929): 0.070001, ((Cgu/Can_colobus: 0.043878, Pne_langur: 0.052150): 0.079045, Mmu_rhesus: 0.019488): 0.043879, (Ssc_squirrelM: 0.041033, Cja_marmoset: 0.023779): 0.121307);
233 Detailed output identifying parameters
235 kappa (ts/tv) = 4.56122
237 dN & dS for each branch
239 branch t S N dN/dS dN dS S*dS N*dN
241 8..9 0.070 107.8 282.2 0.6858 0.0207 0.0302 3.3 5.8
242 9..1 0.026 107.8 282.2 0.6858 0.0076 0.0110 1.2 2.1
243 9..2 0.039 107.8 282.2 0.6858 0.0115 0.0168 1.8 3.2
244 8..10 0.044 107.8 282.2 0.6858 0.0130 0.0189 2.0 3.7
245 10..11 0.079 107.8 282.2 3.5057 0.0328 0.0094 1.0 9.3
246 11..3 0.044 107.8 282.2 0.6858 0.0130 0.0189 2.0 3.7
247 11..4 0.052 107.8 282.2 0.6858 0.0154 0.0225 2.4 4.4
248 10..5 0.019 107.8 282.2 0.6858 0.0058 0.0084 0.9 1.6
249 8..12 0.121 107.8 282.2 0.6858 0.0359 0.0523 5.6 10.1
250 12..6 0.041 107.8 282.2 0.6858 0.0121 0.0177 1.9 3.4
251 12..7 0.024 107.8 282.2 0.6858 0.0070 0.0103 1.1 2.0
253 tree length for dN: 0.17485
254 tree length for dS: 0.21644
256 dS tree:
257 ((Hsa_Human: 0.011031, Hla_gibbon: 0.016794): 0.030198, ((Cgu/Can_colobus: 0.018929, Pne_langur: 0.022497): 0.009367, Mmu_rhesus: 0.008407): 0.018929, (Ssc_squirrelM: 0.017702, Cja_marmoset: 0.010258): 0.052331);
258 dN tree:
259 ((Hsa_Human: 0.007565, Hla_gibbon: 0.011517): 0.020710, ((Cgu/Can_colobus: 0.012982, Pne_langur: 0.015429): 0.032838, Mmu_rhesus: 0.005766): 0.012982, (Ssc_squirrelM: 0.012140, Cja_marmoset: 0.007035): 0.035889);
262 Tree comparisons (Kishino & Hasegawa 1989; Shimodaira & Hasegawa 1999)
263 Number of replicates: 10000
265 tree li Dli +- SE pKH pSH pRELL
267 1* -904.637 0.000 0.000 -1.000 -1.000 0.511
268 2 -904.637 -0.000 0.000 0.500 0.516 0.489
270 pKH: P value for KH normal test (Kishino & Hasegawa 1989)
271 pRELL: RELL bootstrap proportions (Kishino & Hasegawa 1989)
272 pSH: P value with multiple-comparison correction (MC in table 1 of Shimodaira & Hasegawa 1999)
273 (-1 for P values means N/A)