How to identify Substitution rate is per time unit in baseml

Question

[aloke205]

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

[aloke205]

I found out the Solution :)

[jxuan]

Hi! How did you solve this problem? I encountered the same problem that there was no substitution rate in mlb file after baseml run. Could you please share your strategy and your solution folder? My email is [e-mail] Thanks so much!

[mdgn]

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

Answer 1

[aloke205]

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

[GenoMax]

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

[aloke205]

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.

[mdgn]

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.

[a.d.young]

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

[a.d.young]

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

[liangna19911314]

Hi @mertdogan and @aloke205 I am suffering the 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 calculate the substitution rate, and I am uanble to detect "Substitution rate is per time unit" in my mld file too

[charles.feigin]

Hi, did you ever find a solution? The baseml.ctl file they link to doesn't actually solve this issue.

[charles.feigin]

The link no longer seems to work. Could you elaborate on your solution?

Edit: the site appears to be hosted at .org rather than .com now, but I tried the provided baseml.ctl file and it made no difference. Still no Substitution Rate line. Could you elaborate more specifically on what the difference was supposed to be here?