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  HyPhy Documentation: Standard Analyses: LocalMolClock.bf

     Summary: Given a nucleotide, aminoacid or codon data file, a tree and a substiution model, LocalMolClock performs the likelihood ratio test of the null hypothesis of local molecular clock, vs the alternative hypothesis of no molecular clock, for every possible subtree of the given tree.. For a binary unrooted tree on N sequences, there are N-3 subtrees. Note that the rooting of the tree has an effect on the composition of subtrees.

     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 each possible subtree. For instance:

 
 ---- RUNNING LOCAL MOLECULAR CLOCKS 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 LOCAL CLOCKS

(*)   - Clock rejected at significance level 0.05
(**)  - Clock rejected at significance level 0.01
(***) - Clock rejected at significance level 0.001

+----------+--------------+-------------+------------+
| Clock At | LR Statistic | Constraints |  P-Value   |
+----------+--------------+-------------+------------+
| Node2    |   0.88675144 |           1 | 0.34635916 |
+----------+--------------+-------------+------------+
| Node1    |   1.19867437 |           2 | 0.54917552 |
+----------+--------------+-------------+------------+

     Result Processing Tools: None applicable.

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