Skip to content

Commit

Permalink
generate new PAML test results
Browse files Browse the repository at this point in the history
  • Loading branch information
@brandoninvergo
brandoninvergo committed Oct 14, 2012
1 parent 231a306 commit 52da146
Showing 1 changed file with 262 additions and 0 deletions.
262 changes: 262 additions & 0 deletions Tests/PAML/Results/yn00/yn00-4_6.out
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,262 @@
5 222

Homo_sapie ATG CCA GTA ATC AAT ATT GAG GAC CTG ACA GAA AAG GAC AAA TTG AAG ATG GAA GTT GAC CAG CTC AAG AAA GAA GTG ACA CTG GAA AGA ATG CTA GTT TCC AAA TGT TGT GAA GAA GTA AGA GAT TAC GTT GAA GAA CGA TCT GGC GAG GAT CCA CTG GTA AAG GGC ATC CCA GAG GAC AAA AAT CCC TTC AAG GAG CTC AAA GGA GGC TGT GTG ATT TCA
Pan_troglo ATG CCA GTA ATC AAT ATT GAG GAC CTG ACA GAA AAG GAC AAA TTG AAG ATG GAA GTT GAC CAG CTC AAG AAA GAA GTG ACA CTG GAA AGA ATG CTA GTT TCC AAA TGC TGT GAA GAA GTA AGA GAT TAC GTT GAA GAA CGA TCT GGC GAG GAT CCA CTG GTA AAG GGC ATC CCA GAG GAC AAA AAT CCC TTC AAG GAG CTC AAA GGA GGC TGT GTG ATT TCA
Gorilla_go ATG CCA GTA ATC AAT ATT GAG GAC CTG ACA GAA AAG GAC AAA TTG AAG ATG GAA GTT GAC CAG CTC AAG AAA GAA GTG ACA CTG GAA AGA ATG CTA GTT TCC AAA TGT TGT GAA GAA GTA AGA GAT TAT GTT GAA GAA CGA TCT GGC GAG GAT CCA CTG GTA AAG GGC ATC CCA GAG GAC AAA AAT CCC TTC AAG GAG CTC AAA GGA GGC TGT GTG ATT TCA
Pongo_pygm ATG CCA GTA ATC AAT ATT GAG GAC CTG ACA GAA AAG GAC AAA TTG AAG ATG GAA GTT GAC CAG CTC AAG AAA GAA GTG ACA CTG GAA AGA ATG CTA GTT TCC AAA TGT TGT GAA GAA GTA AGA GAT TAC GTT GAA GAA CGA TCT GGC GAG GAT CCA CTG GTA AAG GGC ATC CCA GAG GAC AAA AAT CCC TTC AAG GAG CTC AAA GGA GGC TGT GTG ATT TCA
Macaca_mul ATG CCA GTA ATC AAT ATT GAG GAC CTG ACA GAA AAG GAC AAA TTG AAG ATG GAA GTT GAC CAG CTC AAG AAA GAA GTG ACA CTG GAA AGA ATG CTA GTA TCC AAA TGT TGT GAA GAA GTA AGA GAT TAC GTC GAA GAA CGA TCT GGC GAG GAT CCA CTG GTA AAG GGC ATC CCA GAG GAC AAA AAT CCC TTC AAG GAG CTC AAA GGA GGC TGT GTG ATT TCA



Printing out site pattern counts


5 102 P

Homo_sapie AAA AAG AAT ACA AGA ATC ATG ATT CAG CCA CCC CGA CTA CTC CTG GAA GAC GAG GAT GGA GGC GTA GTG GTT GTT GTT TAC TCA TCC TCT TGT TGT TTC TTG
Pan_troglo ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ...
Gorilla_go ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ...
Pongo_pygm ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Macaca_mul ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..C ... ... ... ... ... ... ... ... ...

5 5 2 2 2 2 3 2 1 3 1 1 1 2 3
8 4 4 2 1 3 3 2 1 1 1 1 1 1 1
1 2 1 1

YN00 Alignments/alignment.phylip

ns = 5 ls = 74

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

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

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

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

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

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
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

Codon usage for each species
--------------------------------------------------------------------------------------------------
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
--------------------------------------------------------------------------------------------------


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



(A) Nei-Gojobori (1986) method



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


(B) Yang & Nielsen (2000) method

Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:32-43

(equal weighting of pathways)

seq. seq. S N t kappa omega dN +- SE dS +- SE

2 1 67.3 154.7 0.0136 3.6564 0.0000 -0.0000 +- 0.0000 0.0150 +- 0.0151
3 1 67.4 154.6 0.0136 3.6564 0.0000 -0.0000 +- 0.0000 0.0150 +- 0.0150
3 2 67.3 154.7 0.0276 3.6564 0.0000 -0.0000 +- 0.0000 0.0303 +- 0.0215
4 1 67.3 154.7 -0.0000 3.6564 99.0000 -0.0000 +- 0.0000 -0.0000 +- 0.0000
4 2 67.3 154.7 0.0136 3.6564 0.0000 -0.0000 +- 0.0000 0.0150 +- 0.0151
4 3 67.4 154.6 0.0136 3.6564 0.0000 -0.0000 +- 0.0000 0.0150 +- 0.0150
5 1 66.8 155.2 0.0276 3.6564 0.0000 -0.0000 +- 0.0000 0.0306 +- 0.0218
5 2 66.7 155.3 0.0420 3.6564 0.0000 -0.0000 +- 0.0000 0.0466 +- 0.0272
5 3 67.0 155.0 0.0420 3.6564 0.0000 -0.0000 +- 0.0000 0.0464 +- 0.0271
5 4 66.8 155.2 0.0276 3.6564 0.0000 -0.0000 +- 0.0000 0.0306 +- 0.0218


(C) LWL85, LPB93 & LWLm methods

Li W.-H., C.-I. Wu, Luo (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2: 150-174.
Li W-H (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96-99
Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes - rates and interdependence between the genes. Mol. Biol. Evol. 10:271-281
Yang Z (2006) Computational Molecular Evolution. Oxford University Press, Oxford. Eqs. 2.12 & 2.13

2 (Pan_troglo) vs. 1 (Homo_sapie)

L(i): 143.0 51.0 28.0 sum= 222.0
Ns(i): 0.0000 1.0000 0.0000 sum= 1.0000
Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000
A(i): 0.0000 0.0200 0.0000
B(i): -0.0000 -0.0000 -0.0000
LWL85: dS = 0.0227 dN = 0.0000 w = 0.0000 S = 45.0 N = 177.0
LWL85m: dS = -nan dN = -nan w = -nan S = -nan N = -nan (rho = -nan)
LPB93: dS = 0.0129 dN = 0.0000 w = 0.0000

3 (Gorilla_go) vs. 1 (Homo_sapie)

L(i): 143.0 51.0 28.0 sum= 222.0
Ns(i): 0.0000 1.0000 0.0000 sum= 1.0000
Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000
A(i): 0.0000 0.0200 0.0000
B(i): -0.0000 -0.0000 -0.0000
LWL85: dS = 0.0227 dN = 0.0000 w = 0.0000 S = 45.0 N = 177.0
LWL85m: dS = -nan dN = -nan w = -nan S = -nan N = -nan (rho = -nan)
LPB93: dS = 0.0129 dN = 0.0000 w = 0.0000

3 (Gorilla_go) vs. 2 (Pan_troglo)

L(i): 143.0 51.0 28.0 sum= 222.0
Ns(i): 0.0000 2.0000 0.0000 sum= 2.0000
Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000
A(i): 0.0000 0.0408 0.0000
B(i): -0.0000 -0.0000 -0.0000
LWL85: dS = 0.0463 dN = 0.0000 w = 0.0000 S = 45.0 N = 177.0
LWL85m: dS = -nan dN = -nan w = -nan S = -nan N = -nan (rho = -nan)
LPB93: dS = 0.0264 dN = 0.0000 w = 0.0000

4 (Pongo_pygm) vs. 1 (Homo_sapie)

L(i): 143.0 51.0 28.0 sum= 222.0
Ns(i): 0.0000 0.0000 0.0000 sum= 0.0000
Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000
A(i): 0.0000 0.0000 0.0000
B(i): -0.0000 -0.0000 -0.0000
LWL85: dS = 0.0000 dN = 0.0000 w = -nan S = 45.0 N = 177.0
LWL85m: dS = -nan dN = -nan w = -nan S = -nan N = -nan (rho = -nan)
LPB93: dS = 0.0000 dN = 0.0000 w = -nan

4 (Pongo_pygm) vs. 2 (Pan_troglo)

L(i): 143.0 51.0 28.0 sum= 222.0
Ns(i): 0.0000 1.0000 0.0000 sum= 1.0000
Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000
A(i): 0.0000 0.0200 0.0000
B(i): -0.0000 -0.0000 -0.0000
LWL85: dS = 0.0227 dN = 0.0000 w = 0.0000 S = 45.0 N = 177.0
LWL85m: dS = -nan dN = -nan w = -nan S = -nan N = -nan (rho = -nan)
LPB93: dS = 0.0129 dN = 0.0000 w = 0.0000

4 (Pongo_pygm) vs. 3 (Gorilla_go)

L(i): 143.0 51.0 28.0 sum= 222.0
Ns(i): 0.0000 1.0000 0.0000 sum= 1.0000
Nv(i): 0.0000 0.0000 0.0000 sum= 0.0000
A(i): 0.0000 0.0200 0.0000
B(i): -0.0000 -0.0000 -0.0000
LWL85: dS = 0.0227 dN = 0.0000 w = 0.0000 S = 45.0 N = 177.0
LWL85m: dS = -nan dN = -nan w = -nan S = -nan N = -nan (rho = -nan)
LPB93: dS = 0.0129 dN = 0.0000 w = 0.0000

5 (Macaca_mul) vs. 1 (Homo_sapie)

L(i): 143.0 51.0 28.0 sum= 222.0
Ns(i): 0.0000 0.0000 1.0000 sum= 1.0000
Nv(i): 0.0000 0.0000 1.0000 sum= 1.0000
A(i): 0.0000 0.0000 0.0381
B(i): -0.0000 -0.0000 0.0371
LWL85: dS = 0.0468 dN = 0.0000 w = 0.0000 S = 45.0 N = 177.0
LWL85m: dS = 0.0391 dN = 0.0000 w = 0.0000 S = 53.9 N = 168.1 (rho = 0.507)
LPB93: dS = 0.0506 dN = 0.0000 w = 0.0000

5 (Macaca_mul) vs. 2 (Pan_troglo)

L(i): 143.0 51.0 28.0 sum= 222.0
Ns(i): 0.0000 1.0000 1.0000 sum= 2.0000
Nv(i): 0.0000 0.0000 1.0000 sum= 1.0000
A(i): 0.0000 0.0200 0.0381
B(i): -0.0000 -0.0000 0.0371
LWL85: dS = 0.0695 dN = 0.0000 w = 0.0000 S = 45.0 N = 177.0
LWL85m: dS = 0.0580 dN = 0.0000 w = 0.0000 S = 53.9 N = 168.1 (rho = 0.507)
LPB93: dS = 0.0635 dN = 0.0000 w = 0.0000

5 (Macaca_mul) vs. 3 (Gorilla_go)

L(i): 143.0 51.0 28.0 sum= 222.0
Ns(i): 0.0000 1.0000 1.0000 sum= 2.0000
Nv(i): 0.0000 0.0000 1.0000 sum= 1.0000
A(i): 0.0000 0.0200 0.0381
B(i): -0.0000 -0.0000 0.0371
LWL85: dS = 0.0695 dN = 0.0000 w = 0.0000 S = 45.0 N = 177.0
LWL85m: dS = 0.0580 dN = 0.0000 w = 0.0000 S = 53.9 N = 168.1 (rho = 0.507)
LPB93: dS = 0.0635 dN = 0.0000 w = 0.0000

5 (Macaca_mul) vs. 4 (Pongo_pygm)

L(i): 143.0 51.0 28.0 sum= 222.0
Ns(i): 0.0000 0.0000 1.0000 sum= 1.0000
Nv(i): 0.0000 0.0000 1.0000 sum= 1.0000
A(i): 0.0000 0.0000 0.0381
B(i): -0.0000 -0.0000 0.0371
LWL85: dS = 0.0468 dN = 0.0000 w = 0.0000 S = 45.0 N = 177.0
LWL85m: dS = 0.0391 dN = 0.0000 w = 0.0000 S = 53.9 N = 168.1 (rho = 0.507)
LPB93: dS = 0.0506 dN = 0.0000 w = 0.0000

0 comments on commit 52da146

Please sign in to comment.