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CODONML (in paml 3.15, November 2005) test.phy Model: One dN/dS ratio
Codon frequencies: F3x4
Site-class models:
ns = 3 ls = 6
Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT 1 1 1 | Ser TCT 1 1 0 | Tyr TAT 0 0 0 | Cys TGT 0 0 0
TTC 0 0 0 | TCC 0 0 1 | TAC 0 0 0 | TGC 0 0 0
Leu TTA 0 0 0 | TCA 0 0 0 | *** TAA 0 0 0 | *** TGA 0 0 0
TTG 0 0 0 | TCG 0 0 0 | TAG 0 0 0 | Trp TGG 0 0 0
--------------------------------------------------------------------------
Leu CTT 0 0 0 | Pro CCT 0 0 0 | His CAT 1 1 1 | Arg CGT 0 0 0
CTC 0 0 0 | CCC 0 0 1 | CAC 0 0 0 | CGC 0 0 0
CTA 0 0 0 | CCA 1 1 0 | Gln CAA 0 0 0 | CGA 0 0 0
CTG 0 0 0 | CCG 0 0 0 | CAG 0 0 0 | CGG 0 0 0
--------------------------------------------------------------------------
Ile ATT 0 0 0 | Thr ACT 0 0 0 | Asn AAT 0 0 0 | Ser AGT 0 0 0
ATC 0 0 0 | ACC 0 0 0 | AAC 0 0 0 | AGC 0 0 0
ATA 0 0 0 | ACA 0 0 0 | Lys AAA 0 0 0 | Arg AGA 0 0 0
Met ATG 2 1 1 | ACG 0 1 1 | AAG 0 0 0 | AGG 0 0 0
--------------------------------------------------------------------------
Val GTT 0 0 0 | Ala GCT 0 0 0 | Asp GAT 0 0 0 | Gly GGT 0 0 0
GTC 0 0 0 | GCC 0 0 0 | GAC 0 0 0 | GGC 0 0 0
GTA 0 0 0 | GCA 0 0 0 | Glu GAA 0 0 0 | GGA 0 0 0
GTG 0 0 0 | GCG 0 0 0 | GAG 0 0 0 | GGG 0 0 0
--------------------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: test0
position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000
position 2: T:0.50000 C:0.33333 A:0.16667 G:0.00000
position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333
#2: test1
position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000
position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000
position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333
#3: test2
position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000
position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000
position 3: T:0.33333 C:0.33333 A:0.00000 G:0.33333
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 3 | Ser S TCT 2 | Tyr Y TAT 0 | Cys C TGT 0
TTC 0 | TCC 1 | TAC 0 | TGC 0
Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0
TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0
------------------------------------------------------------------------------
Leu L CTT 0 | Pro P CCT 0 | His H CAT 3 | Arg R CGT 0
CTC 0 | CCC 1 | CAC 0 | CGC 0
CTA 0 | CCA 2 | Gln Q CAA 0 | CGA 0
CTG 0 | CCG 0 | CAG 0 | CGG 0
------------------------------------------------------------------------------
Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0
ATC 0 | ACC 0 | AAC 0 | AGC 0
ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0
Met M ATG 4 | ACG 2 | AAG 0 | AGG 0
------------------------------------------------------------------------------
Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0
GTC 0 | GCC 0 | GAC 0 | GGC 0
GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0
GTG 0 | GCG 0 | GAG 0 | GGG 0
------------------------------------------------------------------------------
Codon position x base (3x4) table, overall
position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000
position 2: T:0.38889 C:0.44444 A:0.16667 G:0.00000
position 3: T:0.44444 C:0.11111 A:0.11111 G:0.33333
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.)
test0
test1 -1.0000 (0.0706 0.0000)
test2 0.0510 (0.0706 1.3844) 0.0000 (0.0000 0.9745)
Model 0: one-ratio
TREE # 1: (1, 2, 3); MP score: 3
lnL(ntime: 3 np: 5): -30.819156 +0.000000
4..1 4..2 4..3
0.25573 0.00000 0.62424 5.28487 0.09213
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.87997
(1: 0.255727, 2: 0.000004, 3: 0.624239);
(test0: 0.255727, test1: 0.000004, test2: 0.624239);
Detailed output identifying parameters
kappa (ts/tv) = 5.28487
omega (dN/dS) = 0.09213
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
4..1 0.256 12.9 5.1 0.0921 0.0224 0.2429 0.3 1.2
4..2 0.000 12.9 5.1 0.0921 0.0000 0.0000 0.0 0.0
4..3 0.624 12.9 5.1 0.0921 0.0546 0.5930 0.7 3.0
tree length for dN: 0.07702
tree length for dS: 0.83594
Time used: 0:00
Model 1: NearlyNeutral (2 categories)
TREE # 1: (1, 2, 3); MP score: 3
lnL(ntime: 3 np: 6): -30.819157 +0.000000
4..1 4..2 4..3
0.25573 0.00000 0.62424 5.28488 1.00000 0.09213
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.87997
(1: 0.255727, 2: 0.000004, 3: 0.624240);
(test0: 0.255727, test1: 0.000004, test2: 0.624240);
Detailed output identifying parameters
kappa (ts/tv) = 5.28488
dN/dS for site classes (K=2)
p: 1.00000 0.00000
w: 0.09213 1.00000
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
4..1 0.256 12.9 5.1 0.0921 0.0224 0.2429 0.3 1.2
4..2 0.000 12.9 5.1 0.0921 0.0000 0.0000 0.0 0.0
4..3 0.624 12.9 5.1 0.0921 0.0546 0.5930 0.7 3.0
Naive Empirical Bayes (NEB) analysis
Time used: 0:02
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