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  HyPhy Documentation: Standard Analyses: MolecularClock.bf

     Summary: Given a nucleotide, aminoacid or codon data file, a tree and a substiution model, MolecularClock performs the likelihood ratio test of the null hypothesis of global molecular clock, vs the alternative hypothesis of no molecular clock.

     Input: A nucleotide, aminoacid or codon data file in any recognizable format. HYPHY uses the following table to translate nucleotide ambiguities (or aminoacid characters). For codon files, any of the predefined genetic code translation tables can be used to interpret the data.
    A starting tree is also needed. It may either be present in the data file, or reside in a separate (Newick string) file.
    The user will be prompted to choose which parameter to impose the clock on, if the model has more than one parameter per branch.

    Models: Any of the standard nucleotide, aminoacid or codon models can be selected for the analysis.

    Output: MolecularClock prints out the results for the null hypothesis (CLOCK), the alternative hypotheis (NO CLOCK), and the likelihood ratio test, including the asymptotic p-value. For instance:

 ---- RUNNING MOLECULAR CLOCK ANALYSIS ---- 
The following data was read:
5 species:{Human,Chimpanzee,Gorilla,Orangutan,Gibbon};
Total Sites:895;
Distinct Sites:85


A tree was found in the data file:
(((Human,Chimpanzee),Gorilla),Orangutan,Gibbon)

Would you like to use it:(Y/N)?y



*-----------------------------------------------------------*
RESULTS WITHOUT THE CLOCK:
Log Likelihood = -2665.4247104919;
Shared Parameters:
R=9.31366

Tree givenTree=(((Human:0.0413464,Chimpanzee:0.0537564)Node2:0.0174517,
Gorilla:0.0575729)Node1:0.0530033,Orangutan:0.100118,Gibbon:0.138923);
*-----------------------------------------------------------*

RESULTS WITH THE CLOCK:
Log Likelihood = -2667.80577630627;
Shared Parameters:
R=9.25595

Tree clockTree=(((Human:0.0465998,Chimpanzee:0.0465998)Node2:0.0156663,
Gorilla:0.0622661)Node1:0.0551945,Orangutan:0.117461,Gibbon:0.117461);
*-----------------------------------------------------------*

-2(Ln Likelihood Ratio)=4.76213
Constrained parameters:4
P-Value:0.312586

 

     Result Processing Tools: After the analysis is finished, the following options are available in the "Results" submenu of the "Analyses" menu:

      For the first four processing tools HYPHY will present the user with a choice of whether constrained or unconstrained   MLE are desired. "lf" is the unconstrained likelihood function for the data set, "lfConstrained" is the likelihood function with molecular clock constraints in place.

      Bootstrapping tools simulate the data, either parametrically under the null hypothesis, or by sampling with replacemnt (non-parametrically), and compute the likelihood ratio statistic for the simulated sets. The mean, variance and simulated p-value for the LR distributions are reported as well as the values of the LR for each replicate.

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002