Question: How to identify Substitution rate is per time unit in baseml
0
gravatar for aloke205
6 months ago by
aloke20530
aloke20530 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 5 months ago • written 6 months ago by aloke20530

I found out the Solution :)

ADD REPLYlink written 6 months ago by aloke20530

Can you please share the solution? I am having the same problem. There is no substitution rate in the mlb file.

ADD REPLYlink written 5 months ago by mdgn10
0
gravatar for aloke205
5 months ago by
aloke20530
aloke20530 wrote:

Please download the baseml.ctl from http://www.fish-evol.com/mcmctreeExampleVert6/text1Eng.html That will solve your problem :)

ADD COMMENTlink written 5 months ago by aloke20530

The link posted is not working. Can you please check and correct?

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax71k

Link is correct. I don't know why it is not working today. @Mertdogan, if you can share you mail id here, I will send you the complete folder via email.

ADD REPLYlink modified 5 months ago • written 5 months ago by aloke20530
1

Thank you for the offer but I used the older version and I got the sub. rate today. There might be a bug I don't know, another colleague tried his previous (worked) files with the newest version and he had the same problem. Thanks though.

ADD REPLYlink written 5 months ago by mdgn10

Hi @mertdogan,

would it be possible for you to share the older version of PAML you're using with me? I'm running into the same problems and am not able to find an older version online.

Thanks!

my email is andyoung at ucdavis.edu

ADD REPLYlink written 4 months ago by a.d.young0

hello @aloke205,

I just ran into the exact same problem. Would it be possible for you to share the folder you downloaded from fish-evol.com before the website went offline? I'm trying to learn how to use MCMCtree, but it isn't easy with half the tutorials being offline, and the other half broken :).

My email as andyoung at ucdavis.edu.

Thanks!! Andrew

ADD REPLYlink written 4 months ago by a.d.young0
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