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  HyPhy Documentation: Standard Analyses: PairwiseRelativeRatio.bf

     Summary: Given an index file, PairwiseRelativeRatio.bf performs a likelihood ratio test, as in RelativeRatio.bf on all possible pair of files in the list.

     Input: An index file containing the list of data files to be included in the analysis. Each line in an index file is a path specifying one data file. A path can be either absolute, or relative to the directory "TemplateBatchFiles" in the HYPHY directory. For example, if "data" is a subdirectory of the HYPHY directory, then index file:

	../data/file01.dat
	../data/file02.dat
	../data/file03.dat
refer to files "file01.dat","file02.dat" and "file03.dat" located in the "data" directory.

When analyzing codon data, it is possible to request that each file be translated using its own genetic code. In order to do that, select "Different Codes" when HYPHY prompts you about genetic codes and modify your index file to include the number of the genetic code on the line following the path to the data file.

	../data/file01.dat
	0
	../data/file02.dat
	1
	../data/file03.dat
	0
The index file above instructs HYPHY to use genetic code 0 (universal) for files "file01.dat" and "file03.dat", and code 1 (mammalian mtDNA) for file "file02.dat". Refer to the list of genetic codes to determine which number references what code. Number '0' references the first genetic code, '1' - the second etc...

     Models: Any of the standard nucleotide, aminoacid or codon models can be selected for the analysis, based on the sequence type. If the model used in the relative rate analysis had two or more parameters per branch, the user is prompted to select which of the parameters to constrain.

     Output: HYPHY generates a complete report for all analyses as a comma-separated file. A sample of on-screen output follows:



***** RUNNING SINGLE FILE ANALYSES *****


File ../data/alpha01.mus : ln-likelihood = -1267.270615
File ../data/alpha02.mus : ln-likelihood = -1273.015812
File ../data/alpha03.mus : ln-likelihood = -1334.600018
File ../data/alpha04.mus : ln-likelihood = -1259.706684
File ../data/alpha05.mus : ln-likelihood = -1230.777447

***** RUNNING PAIRWISE CONSTRAINED ANALYSES (15 PAIR) *****

***** ESTIMATED TIME TO COMPLETE ALL ANALYSES: 0 hours, 1 minutes. *****



 In the summary table below

 (*)   corresponds to the .05 significance level
 (**)  corresponds to the .01 significance level
 (***) corresponds to the .001 significance level.

+--------+--------+--------------+--------------+
| File 1 | File 2 |      LRT     |    P-Value   |
+--------+--------+--------------+--------------+
|      1 |      2 |      6.84920 |   0.65281657 |
|      1 |      3 |      8.07561 |   0.52654466 |
|      1 |      4 |      5.99568 |   0.74035040 |
|      1 |      5 |      8.68861 |   0.46650047 |
|      2 |      3 |      9.62111 |   0.38201964 |
|      2 |      4 |     14.93676 |   0.09268783 |
|      2 |      5 |     23.07619 |   0.00602746 | (**) 
|      3 |      4 |     12.57365 |   0.18286575 |
|      3 |      5 |     17.20462 |   0.04560644 | (*) 
|      4 |      5 |     13.45110 |   0.14323382 |
+--------+--------+--------------+--------------+

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