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  HyPhy Documentation: Standard Analyses: MolClockAllRoots.bf

     Summary: Given a nucleotide, aminoacid or codon data file, a tree and a substiution model, MolClockAllRoots performs the likelihood ratio test of the null hypothesis of global molecular clock, vs the alternative hypothesis of no molecular clock, on every possible rooted version of the tree. For a binary unrooted tree on N sequences, there are 2N-3 possible rootings.

     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 rooting. 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 FOR DIFFERENT ROOTINGS

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

+-------------+--------------+-------------+------------+
| Rooted At   | LR Statistic | Constraints |  P-Value   |
+-------------+--------------+-------------+------------+
| Node2       |  45.91174882 |           3 | 0.00000000 | (***)
+-------------+--------------+-------------+------------+
| Node1       |   4.68126674 |           3 | 0.19668047 |
+-------------+--------------+-------------+------------+
| Human       |  77.90868274 |           3 | 0.00000000 | (***)
+-------------+--------------+-------------+------------+
| Chimpanzee  |  95.91928481 |           3 | 0.00000000 | (***)
+-------------+--------------+-------------+------------+
| Gorilla     |  49.92279344 |           3 | 0.00000000 | (***)
+-------------+--------------+-------------+------------+
| Orangutan   |   2.60993791 |           3 | 0.45574997 |
+-------------+--------------+-------------+------------+
| Gibbon      |   1.81583411 |           3 | 0.61149533 |
+-------------+--------------+-------------+------------+

     Result Processing Tools: None applicable.

 
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