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
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
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
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
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
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
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
CODONML (in paml 3.13, August 2002) lysozymeSmall.txt Model: One dN/dS ratio dGamma (ncatG=11)
Codon frequencies: F3x4
Warning: Gamma model for codons. See documentation.Site-class models
ns = 7 ls = 130
# site patterns = 81
2 1 1 1 2 7 2 3 3 1 2 2 2 1 1
5 1 4 3 2 1 1 3 1 5 4 5 1 1 1
1 2 1 3 2 1 1 1 1 1 1 1 2 2 1
1 1 1 1 1 2 2 1 1 1 1 1 1 3 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1
1
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
Hla_gibbon ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ..C ... ... ... ... ..C ... ... ... ... ... ... ... C.. ... ... A.. ... ... ..A
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
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.. ... ...
Mmu_rhesus ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... G.. ... AA. ..T ... .A. ... ... C.. ... CA. ... ... ... ... ... ... .A. ... ... A.. ... ... ... ... ... ... A.. ... ... .A. ... ... ... ... ... ... A.. ... A.. ... ... ... ... ... .AC ... ... A.. ... ... ... ... ...
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
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
Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
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
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
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
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
--------------------------------------------------------------------------------------------------------------
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
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
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
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
--------------------------------------------------------------------------------------------------------------
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
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
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
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
--------------------------------------------------------------------------------------------------------------
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
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
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
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
--------------------------------------------------------------------------------------------------------------
--------------------------------------------------
Phe TTT 3 | Ser TCT 0 | Tyr TAT 4 | Cys TGT 7
TTC 0 | TCC 1 | TAC 2 | TGC 1
Leu TTA 0 | TCA 0 | *** TAA 0 | *** TGA 0
TTG 3 | TCG 0 | TAG 0 | Trp TGG 5
--------------------------------------------------
Leu CTT 0 | Pro CCT 1 | His CAT 2 | Arg CGT 1
CTC 0 | CCC 0 | CAC 1 | CGC 1
CTA 1 | CCA 2 | Gln CAA 5 | CGA 0
CTG 3 | CCG 0 | CAG 2 | CGG 0
--------------------------------------------------
Ile ATT 1 | Thr ACT 3 | Asn AAT 5 | Ser AGT 2
ATC 3 | ACC 1 | AAC 5 | AGC 3
ATA 2 | ACA 2 | Lys AAA 3 | Arg AGA 3
Met ATG 1 | ACG 0 | AAG 2 | AGG 5
--------------------------------------------------
Val GTT 3 | Ala GCT 4 | Asp GAT 6 | Gly GGT 1
GTC 3 | GCC 4 | GAC 2 | GGC 3
GTA 1 | GCA 5 | Glu GAA 2 | GGA 5
GTG 2 | GCG 0 | GAG 2 | GGG 1
--------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: Hsa_Human
position 1: T:0.20769 C:0.13077 A:0.31538 G:0.34615
position 2: T:0.20000 C:0.16923 A:0.30000 G:0.33077
position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231
#2: Hla_gibbon
position 1: T:0.20769 C:0.14615 A:0.32308 G:0.32308
position 2: T:0.20000 C:0.16923 A:0.30769 G:0.32308
position 3: T:0.32308 C:0.23077 A:0.26154 G:0.18462
#3: Cgu/Can_colobus
position 1: T:0.20000 C:0.12308 A:0.32308 G:0.35385
position 2: T:0.20000 C:0.16923 A:0.35385 G:0.27692
position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231
#4: Pne_langur
position 1: T:0.20000 C:0.12308 A:0.31538 G:0.36154
position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462
position 3: T:0.31538 C:0.23846 A:0.25385 G:0.19231
#5: Mmu_rhesus
position 1: T:0.20000 C:0.13846 A:0.34615 G:0.31538
position 2: T:0.20000 C:0.16923 A:0.34615 G:0.28462
position 3: T:0.33077 C:0.22308 A:0.25385 G:0.19231
#6: Ssc_squirrelM
position 1: T:0.19231 C:0.15385 A:0.32308 G:0.33077
position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231
position 3: T:0.33077 C:0.23077 A:0.24615 G:0.19231
#7: Cja_marmoset
position 1: T:0.20000 C:0.14615 A:0.31538 G:0.33846
position 2: T:0.20000 C:0.17692 A:0.33077 G:0.29231
position 3: T:0.33077 C:0.23077 A:0.23846 G:0.20000
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 14 | Ser S TCT 0 | Tyr Y TAT 21 | Cys C TGT 49
TTC 1 | TCC 7 | TAC 21 | TGC 7
Leu L TTA 2 | TCA 0 | *** * TAA 0 | *** * TGA 0
TTG 26 | TCG 0 | TAG 0 | Trp W TGG 35
------------------------------------------------------------------------------
Leu L CTT 1 | Pro P CCT 6 | His H CAT 9 | Arg R CGT 8
CTC 1 | CCC 0 | CAC 6 | CGC 6
CTA 7 | CCA 14 | Gln Q CAA 31 | CGA 4
CTG 18 | CCG 0 | CAG 14 | CGG 0
------------------------------------------------------------------------------
Ile I ATT 7 | Thr T ACT 17 | Asn N AAT 42 | Ser S AGT 17
ATC 22 | ACC 7 | AAC 35 | AGC 21
ATA 12 | ACA 14 | Lys K AAA 26 | Arg R AGA 28
Met M ATG 7 | ACG 0 | AAG 17 | AGG 22
------------------------------------------------------------------------------
Val V GTT 21 | Ala A GCT 32 | Asp D GAT 43 | Gly G GGT 11
GTC 19 | GCC 24 | GAC 10 | GGC 21
GTA 9 | GCA 35 | Glu E GAA 12 | GGA 35
GTG 15 | GCG 0 | GAG 14 | GGG 7
------------------------------------------------------------------------------
Codon position x base (3x4) table, overall
position 1: T:0.20110 C:0.13736 A:0.32308 G:0.33846
position 2: T:0.20000 C:0.17143 A:0.33077 G:0.29780
position 3: T:0.32747 C:0.22857 A:0.25165 G:0.19231
Codon frequencies under model, for use in evolver:
0.01378574 0.00962226 0.01059374 0.00809565
0.01181635 0.00824765 0.00908035 0.00693913
0.02279949 0.01591374 0.00000000 0.00000000
0.02052711 0.01432765 0.00000000 0.01205451
0.00941649 0.00657258 0.00723616 0.00552982
0.00807127 0.00563364 0.00620242 0.00473984
0.01557342 0.01087004 0.01196749 0.00914546
0.01402125 0.00978665 0.01077472 0.00823396
0.02214758 0.01545871 0.01701945 0.01300613
0.01898364 0.01325032 0.01458810 0.01114811
0.03662868 0.02556633 0.02814755 0.02151013
0.03297798 0.02301819 0.02534214 0.01936627
0.02320222 0.01619484 0.01782990 0.01362547
0.01988762 0.01388129 0.01528277 0.01167897
0.03837291 0.02678377 0.02948791 0.02253443
0.03454836 0.02411429 0.02654891 0.02028847
Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)
Hsa_Human
Hla_gibbon 0.2782 (0.0133 0.0478)
Cgu/Can_colobus 1.1086 (0.0742 0.0670) 1.1055 (0.0742 0.0671)
Pne_langur 1.1979 (0.0725 0.0605) 0.9234 (0.0797 0.0863) 0.5517 (0.0267 0.0484)
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)
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)
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)
Model 0: one-ratio
TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65
check convergence..
lnL(ntime: 11 np: 14): -906.017440 +0.000000
8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7
0.06798 0.02556 0.03889 0.04345 0.07637 0.04379 0.05254 0.02168 0.12266 0.04080 0.02392 4.54006 0.80663 0.50000
SEs for parameters:
0.02557 0.01516 0.01844 0.02016 0.02668 0.01990 0.02155 0.01551 0.03392 0.01916 0.01506 0.23600 0.23600 -1.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.55765
((1: 0.02556, 2: 0.03889): 0.06798, ((3: 0.04379, 4: 0.05254): 0.07637, 5: 0.02168): 0.04345, (6: 0.04080, 7: 0.02392): 0.12266);
((Hsa_Human: 0.02556, Hla_gibbon: 0.03889): 0.06798, ((Cgu/Can_colobus: 0.04379, Pne_langur: 0.05254): 0.07637, Mmu_rhesus: 0.02168): 0.04345, (Ssc_squirrelM: 0.04080, Cja_marmoset: 0.02392): 0.12266);
Detailed output identifying parameters
kappa (ts/tv) = 4.54006
alpha (gamma) = 0.50000
r ( 1): 1.00000
f: 1.00000
dN & dS for each branch
branch t S N dN/dS dN dS S*dS N*dN
8..9 0.068 107.8 282.2 0.8066 0.0213 0.0263 2.8 6.0
9..1 0.026 107.8 282.2 0.8066 0.0080 0.0099 1.1 2.3
9..2 0.039 107.8 282.2 0.8066 0.0122 0.0151 1.6 3.4
8..10 0.043 107.8 282.2 0.8066 0.0136 0.0168 1.8 3.8
10..11 0.076 107.8 282.2 0.8066 0.0239 0.0296 3.2 6.7
11..3 0.044 107.8 282.2 0.8066 0.0137 0.0170 1.8 3.9
11..4 0.053 107.8 282.2 0.8066 0.0164 0.0204 2.2 4.6
10..5 0.022 107.8 282.2 0.8066 0.0068 0.0084 0.9 1.9
8..12 0.123 107.8 282.2 0.8066 0.0383 0.0475 5.1 10.8
12..6 0.041 107.8 282.2 0.8066 0.0128 0.0158 1.7 3.6
12..7 0.024 107.8 282.2 0.8066 0.0075 0.0093 1.0 2.1
Time used: 00:02:05
Model 1: neutral (2 categories)
TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65
lnL(ntime: 11 np: 14): -902.503869 +0.000000
8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7
0.06961 0.02556 0.03938 0.04422 0.07778 0.04414 0.05228 0.02134 0.12574 0.04157 0.02367 4.29790 0.41271 0.50000
SEs for parameters:
0.02665 0.01541 0.01888 0.02101 0.02769 0.02034 0.02188 0.01585 0.03565 0.01971 0.01530 -1.00000 -1.00000 -1.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.56528
((1: 0.02556, 2: 0.03938): 0.06961, ((3: 0.04414, 4: 0.05228): 0.07778, 5: 0.02134): 0.04422, (6: 0.04157, 7: 0.02367): 0.12574);
((Hsa_Human: 0.02556, Hla_gibbon: 0.03938): 0.06961, ((Cgu/Can_colobus: 0.04414, Pne_langur: 0.05228): 0.07778, Mmu_rhesus: 0.02134): 0.04422, (Ssc_squirrelM: 0.04157, Cja_marmoset: 0.02367): 0.12574);
Detailed output identifying parameters
kappa (ts/tv) = 4.29790
dN/dS for site classes (K=2)
p: 0.41271 0.58729
w: 0.00000 1.00000
alpha (gamma) = 0.41271
r ( 2): 0.00000 1.00000
f: 0.41271 0.58729
dN & dS for each branch
branch t S N dN/dS dN dS S*dS N*dN
8..9 0.070 107.1 282.9 0.5873 0.0195 0.0331 3.5 5.5
9..1 0.026 107.1 282.9 0.5873 0.0071 0.0122 1.3 2.0
9..2 0.039 107.1 282.9 0.5873 0.0110 0.0187 2.0 3.1
8..10 0.044 107.1 282.9 0.5873 0.0124 0.0210 2.3 3.5
10..11 0.078 107.1 282.9 0.5873 0.0217 0.0370 4.0 6.1
11..3 0.044 107.1 282.9 0.5873 0.0123 0.0210 2.2 3.5
11..4 0.052 107.1 282.9 0.5873 0.0146 0.0249 2.7 4.1
10..5 0.021 107.1 282.9 0.5873 0.0060 0.0102 1.1 1.7
8..12 0.126 107.1 282.9 0.5873 0.0351 0.0598 6.4 9.9
12..6 0.042 107.1 282.9 0.5873 0.0116 0.0198 2.1 3.3
12..7 0.024 107.1 282.9 0.5873 0.0066 0.0113 1.2 1.9
Time used: 00:05:26
Model 2: selection (3 categories)
TREE # 1: ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65
check convergence..
lnL(ntime: 11 np: 16): -900.076500 +0.000000
8..9 9..1 9..2 8..10 10..11 11..3 11..4 10..5 8..12 12..6 12..7
0.07903 0.02598 0.04137 0.04535 0.08550 0.04486 0.05417 0.01935 0.13948 0.04319 0.02492 5.12250 0.38160 0.54916 6.17292 0.41271
SEs for parameters:
0.03226 0.01618 0.02021 0.02390 0.03229 0.02158 0.02363 0.01746 0.04358 0.02088 0.01602 1.50414 0.14016 0.16630 4.30113 -1.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.60321
((1: 0.02598, 2: 0.04137): 0.07903, ((3: 0.04486, 4: 0.05417): 0.08550, 5: 0.01935): 0.04535, (6: 0.04319, 7: 0.02492): 0.13948);
((Hsa_Human: 0.02598, Hla_gibbon: 0.04137): 0.07903, ((Cgu/Can_colobus: 0.04486, Pne_langur: 0.05417): 0.08550, Mmu_rhesus: 0.01935): 0.04535, (Ssc_squirrelM: 0.04319, Cja_marmoset: 0.02492): 0.13948);
Detailed output identifying parameters
kappa (ts/tv) = 5.12250
dN/dS for site classes (K=3)
p: 0.38160 0.54916 0.06924
w: 0.00000 1.00000 6.17292
alpha (gamma) = 0.38160
r ( 3): 0.00000 1.00000 6.17292
f: 0.38160 0.54916 0.06924
dN & dS for each branch
branch t S N dN/dS dN dS S*dS N*dN
8..9 0.079 109.3 280.7 0.9766 0.0262 0.0268 2.9 7.3
9..1 0.026 109.3 280.7 0.9766 0.0086 0.0088 1.0 2.4
9..2 0.041 109.3 280.7 0.9766 0.0137 0.0140 1.5 3.8
8..10 0.045 109.3 280.7 0.9766 0.0150 0.0154 1.7 4.2
10..11 0.086 109.3 280.7 0.9766 0.0283 0.0290 3.2 7.9
11..3 0.045 109.3 280.7 0.9766 0.0149 0.0152 1.7 4.2
11..4 0.054 109.3 280.7 0.9766 0.0179 0.0184 2.0 5.0
10..5 0.019 109.3 280.7 0.9766 0.0064 0.0066 0.7 1.8
8..12 0.139 109.3 280.7 0.9766 0.0462 0.0473 5.2 13.0
12..6 0.043 109.3 280.7 0.9766 0.0143 0.0146 1.6 4.0
12..7 0.025 109.3 280.7 0.9766 0.0083 0.0085 0.9 2.3
Positively selected sites Prob(w>1):
15 L 0.6588
17 M 0.6601
37 G 0.7155
41 R 0.9282
50 R 0.8292
62 R 0.5229
114 N 0.6491
126 Q 0.5226
Time used: 00:13:43