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.
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