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How to identify Substitution rate is per time unit in baseml
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21 months ago
aloke205 • 30
@aloke20550654

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

codeml baseml substitution rate • 295 views
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I found out the Solution :)

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

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21 months ago
aloke205 • 30
@aloke20550654

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

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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.

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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.

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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

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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

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