Entering edit mode
5.9 years ago
sunnykevin97
▴
990
Hi
I runned PAML with example dataset , to estimate the dN/dS ratio It generate some output not to able interpret the results ?
Is it possible to run PAML using null and alternative models ? If so, what the options do I need to add ?
Here is codeml.ctl file
seqfile = sample.nuc * sequence data filename
treefile = sample.trees * tree structure file name
outfile = sample.mlc * main result file name
noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
verbose = 1 * 0: concise; 1: detailed, 2: too much
runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
* 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
seqtype = 2 * 1:codons; 2:AAs; 3:codons-->AAs
CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
* ndata = 10
clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
aaRatefile = dat/jones.dat * only used for aa seqs with model=empirical(_F)
* dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
model = 2
* models for codons:
* 0:one, 1:b, 2:2 or more dN/dS ratios for branches
* models for AAs or codon-translated AAs:
* 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
* 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)
NSsites = 0 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
* 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
* 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
* 13:3normal>0
icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below
Mgene = 0
* codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
* AA: 0:rates, 1:separate
fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
kappa = 2 * initial or fixed kappa
fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
omega = .4 * initial or fixed omega, for codons or codon-based AAs
fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
alpha = 0. * initial or fixed alpha, 0:infinity (constant rate)
Malpha = 0 * different alphas for genes
ncatG = 8 * # of categories in dG of NSsites models
getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
Small_Diff = .5e-6
cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)?
* fix_blength = -1 * 0: ignore, -1: random, 1: initial, 2: fixed
method = 0 * Optimization method 0: simultaneous; 1: one branch a time
* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt.,
* 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt.,
* 10: blepharisma nu.
* These codes correspond to transl_table 1 to 11 of GENEBANK.
Output ==> sample.mlc file
3 120
Mprimige TTT GTT GAT TTC AAA GAC CAG GAG TGG AAG AAA GCT ACT GCA ACT CAT GCA AAT GAC ACA ATT ATT GCT TAC AAA GAC CAG GAG TGG AAG AAA GCT ACT GCA ACT CAT GCA AAT GAC ACA
Emaximus TTT ATT GCT TAC AAA GAC CAG GAG TGG AAG AAA GCT ACT GCA ACT CAT GCA AAT GAC ACA ATT ATT GCT TAC AAA GAC CAG GAG TGG AAG AAA GCT ACT GCA ACT CAT GCA AAT GAC ACA
Lafrican ATT ATT GCT TAC AAA GAC CAG GAG TGG AAG AAA GCT ACT GCA ACT CAT GCA AAT GAC ACA ATT ATT GCT TAC AAA GAC CAG GAG TGG AAG AAA GCT ACT GCA ACT CAT GCA AAT GAC ACA
Printing out site pattern counts
3 54 P
Mprimige AAA AAG AAT ACA ACT ATT CAG CAT GAC GAG GAT GCA GCT GTT TAC TGG TTC TTT
Emaximus ... ... ... ... ... ... ... ... ... ... .C. ... ... A.. ... ... .A. ...
Lafrican ... ... ... ... ... ... ... ... ... ... .C. ... ... A.. ... ... .A. A..
4 2 2 2 4 2 2 2 4 2 1 4 3 1 1
2 1 1
CODONML (in paml version 4.9e, April 2017) elephant.nuc
Model: several dN/dS ratios for branches for branches,
Codon frequency model: F3x4
ns = 3 ls = 40
Codon usage in sequences
--------------------------------------------------------------------------------------
Phe TTT 1 1 0 | Ser TCT 0 0 0 | Tyr TAT 0 0 0 | Cys TGT 0 0 0
TTC 1 0 0 | TCC 0 0 0 | TAC 1 2 2 | 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 2 2 2
--------------------------------------------------------------------------------------
Leu CTT 0 0 0 | Pro CCT 0 0 0 | His CAT 2 2 2 | Arg CGT 0 0 0
CTC 0 0 0 | CCC 0 0 0 | CAC 0 0 0 | CGC 0 0 0
CTA 0 0 0 | CCA 0 0 0 | Gln CAA 0 0 0 | CGA 0 0 0
CTG 0 0 0 | CCG 0 0 0 | CAG 2 2 2 | CGG 0 0 0
--------------------------------------------------------------------------------------
Ile ATT 2 3 4 | Thr ACT 4 4 4 | Asn AAT 2 2 2 | 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 2 2 2 | Lys AAA 4 4 4 | Arg AGA 0 0 0
Met ATG 0 0 0 | ACG 0 0 0 | AAG 2 2 2 | AGG 0 0 0
--------------------------------------------------------------------------------------
Val GTT 1 0 0 | Ala GCT 3 4 4 | Asp GAT 1 0 0 | Gly GGT 0 0 0
GTC 0 0 0 | GCC 0 0 0 | GAC 4 4 4 | GGC 0 0 0
GTA 0 0 0 | GCA 4 4 4 | Glu GAA 0 0 0 | GGA 0 0 0
GTG 0 0 0 | GCG 0 0 0 | GAG 2 2 2 | GGG 0 0 0
--------------------------------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: Mprimige
position 1: T:0.12500 C:0.10000 A:0.40000 G:0.37500
position 2: T:0.12500 C:0.32500 A:0.50000 G:0.05000
position 3: T:0.40000 C:0.15000 A:0.25000 G:0.20000
Average T:0.21667 C:0.19167 A:0.38333 G:0.20833
#2: Emaximus
position 1: T:0.12500 C:0.10000 A:0.42500 G:0.35000
position 2: T:0.10000 C:0.35000 A:0.50000 G:0.05000
position 3: T:0.40000 C:0.15000 A:0.25000 G:0.20000
Average T:0.20833 C:0.20000 A:0.39167 G:0.20000
#3: Lafrican
position 1: T:0.10000 C:0.10000 A:0.45000 G:0.35000
position 2: T:0.10000 C:0.35000 A:0.50000 G:0.05000
position 3: T:0.40000 C:0.15000 A:0.25000 G:0.20000
Average T:0.20000 C:0.20000 A:0.40000 G:0.20000
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 2 | Ser S TCT 0 | Tyr Y TAT 0 | Cys C TGT 0
TTC 1 | TCC 0 | TAC 5 | TGC 0
Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0
TTG 0 | TCG 0 | TAG 0 | Trp W TGG 6
------------------------------------------------------------------------------
Leu L CTT 0 | Pro P CCT 0 | His H CAT 6 | Arg R CGT 0
CTC 0 | CCC 0 | CAC 0 | CGC 0
CTA 0 | CCA 0 | Gln Q CAA 0 | CGA 0
CTG 0 | CCG 0 | CAG 6 | CGG 0
------------------------------------------------------------------------------
Ile I ATT 9 | Thr T ACT 12 | Asn N AAT 6 | Ser S AGT 0
ATC 0 | ACC 0 | AAC 0 | AGC 0
ATA 0 | ACA 6 | Lys K AAA 12 | Arg R AGA 0
Met M ATG 0 | ACG 0 | AAG 6 | AGG 0
------------------------------------------------------------------------------
Val V GTT 1 | Ala A GCT 11 | Asp D GAT 1 | Gly G GGT 0
GTC 0 | GCC 0 | GAC 12 | GGC 0
GTA 0 | GCA 12 | Glu E GAA 0 | GGA 0
GTG 0 | GCG 0 | GAG 6 | GGG 0
------------------------------------------------------------------------------
Codon position x base (3x4) table, overall
position 1: T:0.11667 C:0.10000 A:0.42500 G:0.35833
position 2: T:0.10833 C:0.34167 A:0.50000 G:0.05000
position 3: T:0.40000 C:0.15000 A:0.25000 G:0.20000
Average T:0.20833 C:0.19722 A:0.39167 G:0.20278
Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
0.00519963 0.00194986 0.00324977 0.00259981
0.01639883 0.00614956 0.01024927 0.00819941
0.02399829 0.00899936 0.00000000 0.00000000
0.00239983 0.00089994 0.00000000 0.00119991
0.00445682 0.00167131 0.00278552 0.00222841
0.01405614 0.00527105 0.00878509 0.00702807
0.02056996 0.00771373 0.01285622 0.01028498
0.00205700 0.00077137 0.00128562 0.00102850
0.01894150 0.00710306 0.01183844 0.00947075
0.05973859 0.02240197 0.03733662 0.02986930
0.08742233 0.03278337 0.05463895 0.04371116
0.00874223 0.00327834 0.00546390 0.00437112
0.01597029 0.00598886 0.00998143 0.00798514
0.05036783 0.01888794 0.03147989 0.02518392
0.07370902 0.02764088 0.04606814 0.03685451
0.00737090 0.00276409 0.00460681 0.00368545
Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)
Mprimige
Emaximus -1.0000 (0.0319 0.0000)
Lafrican -1.0000 (0.0429 0.0000)-1.0000 (0.0105 0.0000)
