Question: How to identify Substitution rate is per time unit in baseml
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gravatar for aloke205
9 days ago by
aloke20510
aloke20510 wrote:

Dear members, I am new to this world of baseml. I am following the tutorial provided in http://www.fish-evol.com/mcmctreeExampleVert6/text1Eng.html. However, I am uanble to detect "Substitution rate is per time unit" in my mld file. I am writing baseml.ctl and my output file result below. Please help me how to calculate "Substitution rate " from the output file

Baseml.ctl

     seqfile = FBtr0005009.phy
 treefile = phylo.nwk      * tree structure file name
 outfile = FBtr0005009.mlb           * main result file name
    noisy = 2   * 0,1,2,3: how much rubbish on the screen
  verbose = 0   * 1: detailed output, 0: concise output
  runmode = 0   * 0: user tree;  1: semi-automatic;  2: automatic  * 3: StepwiseAddition; (4,5):PerturbationNNI 
    model = 7   * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
                * 5:T92, 6:TN93, 7:REV, 8:UNREST, 9:REVu; 10:UNRESTu
    Mgene = 0   * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
   clock = 1   * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
fix_kappa = 0   * 0: estimate kappa; 1: fix kappa at value below; 2: kappa for branches
    kappa = 5  * initial or fixed kappa

fix_alpha = 0   * 0: estimate alpha; 1: fix alpha at value below
    alpha = 0.5   * initial or fixed alpha, 0:infinity (constant rate)
   Malpha = 0   * 1: different alpha's for genes, 0: one alpha
    ncatG = 5   * # of categories in the dG, AdG, or nparK models of rates
    nparK = 0   * rate-class models. 1:rK, 2:rK&fK, 3:rK&MK(1/K), 4:rK&MK 

    nhomo = 0   * 0 & 1: homogeneous, 2: kappa for branches, 3: N1, 4: N2
    getSE = 0   * 0: don't want them, 1: want S.E.s of estimates
    RateAncestor = 0   * (0,1,2): rates (alpha>0) or ancestral states
     Small_Diff = 7e-6
     cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?

output :

Detailed output identifying parameters

Parameters in the rate matrix (REV) (Yang 1994 J Mol Evol 39:105-111):

Rate parameters: 4.59933 0.49989 0.84105 0.67237 0.70256

Base frequencies: 0.19112 0.29287 0.23249 0.28351

Rate matrix Q, Average Ts/Tv = 1.8811 -1.717963 1.359905 0.117329 0.240729 0.887443 -1.246346 0.157812 0.201091 0.096453 0.198802 -0.581481 0.286225 0.162281 0.207730 0.234711 -0.604722

alpha (gamma, K=5) = 0.26292 rate: 0.00118 0.03217 0.20909 0.83198 3.92557 freq: 0.20000 0.20000 0.20000 0.20000 0.20000

Thanks in advance

ADD COMMENTlink modified 8 days ago • written 9 days ago by aloke20510
0
gravatar for aloke205
8 days ago by
aloke20510
aloke20510 wrote:

I found out the Solution :)

ADD COMMENTlink written 8 days ago by aloke20510
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