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Generate codeml test results for all versions
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@brandoninvergo @peterjc
brandoninvergo authored and peterjc committed Feb 22, 2012
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3 changes: 2 additions & 1 deletion Tests/PAML/Alignments/aa_alignment.phylip
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@@ -1,3 +1,5 @@
5 91

>Homo_sapie
--MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEVRDYVEERS
GEDPLVKGIPEDKNPFKELKGGCVIS---------------
Expand All @@ -13,4 +15,3 @@ GEDPLVKGIPEDKNPFKELKGGCVIS---------------
>Macaca_mul
--MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEVRDYVEERS
GEDPLVKGIPEDKNPFKELKGGCVISKYRKKILNCWKYLKC

131 changes: 131 additions & 0 deletions Tests/PAML/Results/codeml/SE/SE-4_1.out
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seed used = 1024020569
CODONML (in paml version 4.1, August 2008) ../Alignments/alignment.phylip
Model: One dN/dS ratio for branches
Codon frequencies: F3x4
ns = 5 ls = 74

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT 0 0 0 0 0 | Ser TCT 1 1 1 1 1 | Tyr TAT 0 0 1 0 0 | Cys TGT 3 2 3 3 3
TTC 1 1 1 1 1 | TCC 1 1 1 1 1 | TAC 1 1 0 1 1 | TGC 0 1 0 0 0
Leu TTA 0 0 0 0 0 | TCA 1 1 1 1 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0
TTG 1 1 1 1 1 | TCG 0 0 0 0 0 | TAG 0 0 0 0 0 | Trp TGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Leu CTT 0 0 0 0 0 | Pro CCT 0 0 0 0 0 | His CAT 0 0 0 0 0 | Arg CGT 0 0 0 0 0
CTC 2 2 2 2 2 | CCC 1 1 1 1 1 | CAC 0 0 0 0 0 | CGC 0 0 0 0 0
CTA 1 1 1 1 1 | CCA 3 3 3 3 3 | Gln CAA 0 0 0 0 0 | CGA 1 1 1 1 1
CTG 3 3 3 3 3 | CCG 0 0 0 0 0 | CAG 1 1 1 1 1 | CGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Ile ATT 2 2 2 2 2 | Thr ACT 0 0 0 0 0 | Asn AAT 2 2 2 2 2 | Ser AGT 0 0 0 0 0
ATC 2 2 2 2 2 | ACC 0 0 0 0 0 | AAC 0 0 0 0 0 | AGC 0 0 0 0 0
ATA 0 0 0 0 0 | ACA 2 2 2 2 2 | Lys AAA 5 5 5 5 5 | Arg AGA 2 2 2 2 2
Met ATG 3 3 3 3 3 | ACG 0 0 0 0 0 | AAG 5 5 5 5 5 | AGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Val GTT 3 3 3 3 1 | Ala GCT 0 0 0 0 0 | Asp GAT 2 2 2 2 2 | Gly GGT 0 0 0 0 0
GTC 0 0 0 0 1 | GCC 0 0 0 0 0 | GAC 4 4 4 4 4 | GGC 3 3 3 3 3
GTA 3 3 3 3 4 | GCA 0 0 0 0 0 | Glu GAA 8 8 8 8 8 | GGA 1 1 1 1 1
GTG 2 2 2 2 2 | GCG 0 0 0 0 0 | GAG 4 4 4 4 4 | GGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------

Codon position x base (3x4) table for each sequence.

#1: Homo_sapie
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.17568 C:0.20270 A:0.36486 G:0.25676
Average T:0.20270 C:0.16216 A:0.36937 G:0.26577

#2: Pan_troglo
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.16216 C:0.21622 A:0.36486 G:0.25676
Average T:0.19820 C:0.16667 A:0.36937 G:0.26577

#3: Gorilla_go
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.18919 C:0.18919 A:0.36486 G:0.25676
Average T:0.20721 C:0.15766 A:0.36937 G:0.26577

#4: Pongo_pygm
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.17568 C:0.20270 A:0.36486 G:0.25676
Average T:0.20270 C:0.16216 A:0.36937 G:0.26577

#5: Macaca_mul
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.14865 C:0.21622 A:0.37838 G:0.25676
Average T:0.19369 C:0.16667 A:0.37387 G:0.26577

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 0 | Ser S TCT 5 | Tyr Y TAT 1 | Cys C TGT 14
TTC 5 | TCC 5 | TAC 4 | TGC 1
Leu L TTA 0 | TCA 5 | *** * TAA 0 | *** * TGA 0
TTG 5 | TCG 0 | TAG 0 | Trp W TGG 0
------------------------------------------------------------------------------
Leu L CTT 0 | Pro P CCT 0 | His H CAT 0 | Arg R CGT 0
CTC 10 | CCC 5 | CAC 0 | CGC 0
CTA 5 | CCA 15 | Gln Q CAA 0 | CGA 5
CTG 15 | CCG 0 | CAG 5 | CGG 0
------------------------------------------------------------------------------
Ile I ATT 10 | Thr T ACT 0 | Asn N AAT 10 | Ser S AGT 0
ATC 10 | ACC 0 | AAC 0 | AGC 0
ATA 0 | ACA 10 | Lys K AAA 25 | Arg R AGA 10
Met M ATG 15 | ACG 0 | AAG 25 | AGG 0
------------------------------------------------------------------------------
Val V GTT 13 | Ala A GCT 0 | Asp D GAT 10 | Gly G GGT 0
GTC 1 | GCC 0 | GAC 20 | GGC 15
GTA 16 | GCA 0 | Glu E GAA 40 | GGA 5
GTG 10 | GCG 0 | GAG 20 | GGG 0
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.17027 C:0.20541 A:0.36757 G:0.25676
Average T:0.20090 C:0.16306 A:0.37027 G:0.26577

TREE # 1: (((1, 2), 3), 4, 5); MP score: 4
lnL(ntime: 7 np: 9): -308.032217 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000000 0.000000 0.000004 0.013437 0.013431 0.000004 0.027837 1.519234 0.000100
SEs for parameters:
0.00052 0.00052 0.00058 0.01353 0.01353 0.00058 0.01995 1.38727 -1.00000

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length = 0.05471

(((1: 0.000004, 2: 0.013437): 0.000000, 3: 0.013431): 0.000000, 4: 0.000004, 5: 0.027837);

(((Homo_sapie: 0.000004, Pan_troglo: 0.013437): 0.000000, Gorilla_go: 0.013431): 0.000000, Pongo_pygm: 0.000004, Macaca_mul: 0.027837);

Detailed output identifying parameters

kappa (ts/tv) = 1.51923

omega (dN/dS) = 0.00010

dN & dS for each branch

branch t N S dN/dS dN dS N*dN S*dS

6..7 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0
7..8 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0
8..1 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0
8..2 0.013 167.7 54.3 0.0001 0.0000 0.0183 0.0 1.0
7..3 0.013 167.7 54.3 0.0001 0.0000 0.0183 0.0 1.0
6..4 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0
6..5 0.028 167.7 54.3 0.0001 0.0000 0.0379 0.0 2.1

tree length for dN: 0.00001
tree length for dS: 0.07454


Time used: 0:01
10 changes: 5 additions & 5 deletions Tests/PAML/Results/codeml/SE/SE-4_3.out
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@@ -1,6 +1,6 @@

seed used = 896531397
CODONML (in paml version 4.3, August 2009) ../Tests/PAML/alignment.phylip
seed used = 1024020573
CODONML (in paml version 4.3, August 2009) ../Alignments/alignment.phylip
Model: One dN/dS ratio for branches
Codon frequency model: F3x4
ns = 5 ls = 74
Expand Down Expand Up @@ -106,9 +106,9 @@ Macaca_mul 0.0000 (0.0000 0.0421) 0.0000 (0.0000 0.0640) 0.0000 (0.000
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4
lnL(ntime: 7 np: 9): -308.032819 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.013437 0.013431 0.000004 0.027837 1.519162 0.000100
0.000004 0.000004 0.000004 0.013437 0.013431 0.000004 0.027837 1.519185 0.000100
SEs for parameters:
7653690.37591 8000740.81408 7721856.17193 0.18942 3.72223 7448763.94153 0.75207 15.03440 1.48215
4440893.61068 4810946.70622 4601222.38522 0.18104 3.86745 4366838.31025 0.73043 15.21761 1.48395

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

Expand All @@ -120,7 +120,7 @@ tree length = 0.05472

Detailed output identifying parameters

kappa (ts/tv) = 1.51916
kappa (ts/tv) = 1.51918

omega (dN/dS) = 0.00010

Expand Down
143 changes: 143 additions & 0 deletions Tests/PAML/Results/codeml/SE/SE-4_4.out
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@@ -0,0 +1,143 @@

seed used = 1024020577
CODONML (in paml version 4.4, January 2010) ../Alignments/alignment.phylip
Model: One dN/dS ratio for branches
Codon frequency model: F3x4
ns = 5 ls = 74

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT 0 0 0 0 0 | Ser TCT 1 1 1 1 1 | Tyr TAT 0 0 1 0 0 | Cys TGT 3 2 3 3 3
TTC 1 1 1 1 1 | TCC 1 1 1 1 1 | TAC 1 1 0 1 1 | TGC 0 1 0 0 0
Leu TTA 0 0 0 0 0 | TCA 1 1 1 1 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0
TTG 1 1 1 1 1 | TCG 0 0 0 0 0 | TAG 0 0 0 0 0 | Trp TGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Leu CTT 0 0 0 0 0 | Pro CCT 0 0 0 0 0 | His CAT 0 0 0 0 0 | Arg CGT 0 0 0 0 0
CTC 2 2 2 2 2 | CCC 1 1 1 1 1 | CAC 0 0 0 0 0 | CGC 0 0 0 0 0
CTA 1 1 1 1 1 | CCA 3 3 3 3 3 | Gln CAA 0 0 0 0 0 | CGA 1 1 1 1 1
CTG 3 3 3 3 3 | CCG 0 0 0 0 0 | CAG 1 1 1 1 1 | CGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Ile ATT 2 2 2 2 2 | Thr ACT 0 0 0 0 0 | Asn AAT 2 2 2 2 2 | Ser AGT 0 0 0 0 0
ATC 2 2 2 2 2 | ACC 0 0 0 0 0 | AAC 0 0 0 0 0 | AGC 0 0 0 0 0
ATA 0 0 0 0 0 | ACA 2 2 2 2 2 | Lys AAA 5 5 5 5 5 | Arg AGA 2 2 2 2 2
Met ATG 3 3 3 3 3 | ACG 0 0 0 0 0 | AAG 5 5 5 5 5 | AGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Val GTT 3 3 3 3 1 | Ala GCT 0 0 0 0 0 | Asp GAT 2 2 2 2 2 | Gly GGT 0 0 0 0 0
GTC 0 0 0 0 1 | GCC 0 0 0 0 0 | GAC 4 4 4 4 4 | GGC 3 3 3 3 3
GTA 3 3 3 3 4 | GCA 0 0 0 0 0 | Glu GAA 8 8 8 8 8 | GGA 1 1 1 1 1
GTG 2 2 2 2 2 | GCG 0 0 0 0 0 | GAG 4 4 4 4 4 | GGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------

Codon position x base (3x4) table for each sequence.

#1: Homo_sapie
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.17568 C:0.20270 A:0.36486 G:0.25676
Average T:0.20270 C:0.16216 A:0.36937 G:0.26577

#2: Pan_troglo
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.16216 C:0.21622 A:0.36486 G:0.25676
Average T:0.19820 C:0.16667 A:0.36937 G:0.26577

#3: Gorilla_go
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.18919 C:0.18919 A:0.36486 G:0.25676
Average T:0.20721 C:0.15766 A:0.36937 G:0.26577

#4: Pongo_pygm
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.17568 C:0.20270 A:0.36486 G:0.25676
Average T:0.20270 C:0.16216 A:0.36937 G:0.26577

#5: Macaca_mul
position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.14865 C:0.21622 A:0.37838 G:0.25676
Average T:0.19369 C:0.16667 A:0.37387 G:0.26577

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 0 | Ser S TCT 5 | Tyr Y TAT 1 | Cys C TGT 14
TTC 5 | TCC 5 | TAC 4 | TGC 1
Leu L TTA 0 | TCA 5 | *** * TAA 0 | *** * TGA 0
TTG 5 | TCG 0 | TAG 0 | Trp W TGG 0
------------------------------------------------------------------------------
Leu L CTT 0 | Pro P CCT 0 | His H CAT 0 | Arg R CGT 0
CTC 10 | CCC 5 | CAC 0 | CGC 0
CTA 5 | CCA 15 | Gln Q CAA 0 | CGA 5
CTG 15 | CCG 0 | CAG 5 | CGG 0
------------------------------------------------------------------------------
Ile I ATT 10 | Thr T ACT 0 | Asn N AAT 10 | Ser S AGT 0
ATC 10 | ACC 0 | AAC 0 | AGC 0
ATA 0 | ACA 10 | Lys K AAA 25 | Arg R AGA 10
Met M ATG 15 | ACG 0 | AAG 25 | AGG 0
------------------------------------------------------------------------------
Val V GTT 13 | Ala A GCT 0 | Asp D GAT 10 | Gly G GGT 0
GTC 1 | GCC 0 | GAC 20 | GGC 15
GTA 16 | GCA 0 | Glu E GAA 40 | GGA 5
GTG 10 | GCG 0 | GAG 20 | GGG 0
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position 1: T:0.12162 C:0.16216 A:0.31081 G:0.40541
position 2: T:0.31081 C:0.12162 A:0.43243 G:0.13514
position 3: T:0.17027 C:0.20541 A:0.36757 G:0.25676
Average T:0.20090 C:0.16306 A:0.37027 G:0.26577


Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)

Homo_sapie
Pan_troglo 0.0000 (0.0000 0.0207)
Gorilla_go 0.0000 (0.0000 0.0207) 0.0000 (0.0000 0.0421)
Pongo_pygm -1.0000 (0.0000 0.0000) 0.0000 (0.0000 0.0207) 0.0000 (0.0000 0.0207)
Macaca_mul 0.0000 (0.0000 0.0421) 0.0000 (0.0000 0.0640) 0.0000 (0.0000 0.0640) 0.0000 (0.0000 0.0421)


TREE # 1: (((1, 2), 3), 4, 5); MP score: 4
lnL(ntime: 7 np: 9): -308.032819 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.013437 0.013431 0.000004 0.027837 1.519171 0.000100
SEs for parameters:
-1.00000 -1.00000 -1.00000 0.16658 3.13858 -1.00000 0.64607 14.21126 1.47565

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length = 0.05472

(((1: 0.000004, 2: 0.013437): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027837);

(((Homo_sapie: 0.000004, Pan_troglo: 0.013437): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027837);

Detailed output identifying parameters

kappa (ts/tv) = 1.51917

omega (dN/dS) = 0.00010

dN & dS for each branch

branch t N S dN/dS dN dS N*dN S*dS

6..7 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0
7..8 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0
8..1 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0
8..2 0.013 167.7 54.3 0.0001 0.0000 0.0183 0.0 1.0
7..3 0.013 167.7 54.3 0.0001 0.0000 0.0183 0.0 1.0
6..4 0.000 167.7 54.3 0.0001 0.0000 0.0000 0.0 0.0
6..5 0.028 167.7 54.3 0.0001 0.0000 0.0379 0.0 2.1

tree length for dN: 0.0000
tree length for dS: 0.0746


Time used: 0:01

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