Question: How to perform Null and Alternative models using PAML (estimation of dN/dS) ?
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gravatar for sunnykevin97
6 months ago by
sunnykevin9710
sunnykevin9710 wrote:

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)
snp sequence alignment • 292 views
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