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  HyPhy Documentation: Standard Analyses: PairwiseRelativeRate.bf

      Summary: Given 3 nucleotide, aminoacid or codon sequences and a relevant substitution model, PairwiseRelativeRate calculates the MLE for the 3-taxa tree, and then MLE for the 3-taxa tree with parameters along two branches constrained to be equal (the 3rd branch is the outgroup and is estimated independently). A likelihood ratio test is then performed to determine whether the alternative hypothesis (all rates are independent) should be accepted or rejected, with the the null hypothesis being: rates along two given branches are equal. PairwiseRelativeRate performs a LRT for all possible pair of sequences from the user selected datafile, given a fixed outgroup.

     Input: A nucleotide, aminoacid or codon data file in any recognizable format. HYPHY uses the following table to translate nucleotide ambiguities (or aminoacid characters). Any of the predefined genetic code translation tables can be used to interpret codon data. The file must contain at least 3 sequences. HYPHY will prompt the user to choose the sequence which will serve as an outgroup for all susequent analyses. 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.

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

    Output:HYPHY generates on-screen summary and writes a complete report in a comma-separated file suitable for import to a spreadsheet program. A sample of on-screen summary follows:

 In the summary table below, branch lengths denote the expected number of substituions per that branch.

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



  Taxa Triplet                                                       LRT        P-Value 
------------------------------------------------------------------+------------+------------
(Orangutan:0.150652,(Human:0.041036,Chimpanzee:0.057436))         |    1.4633  | 0.481125
(Orangutan:0.139560,(Human:0.052322,Gorilla:0.063556))            |    1.1705  | 0.556969
(Orangutan:0.101987,(Human:0.089062,Gibbon:0.129168))             |    7.6230  | 0.022115 (*) 
------------------------------------------------------------------+------------+------------
(Orangutan:0.146444,(Chimpanzee:0.062931,Gorilla:0.057106))       |    0.2319  | 0.890527
(Orangutan:0.104220,(Chimpanzee:0.103676,Gibbon:0.128611))        |    7.0881  | 0.028896 (*) 
------------------------------------------------------------------+------------+------------
(Orangutan:0.101451,(Gorilla:0.100987,Gibbon:0.130182))           |    8.3502  | 0.015373 (*) 
------------------------------------------------------------------+------------+------------

    Result Processing Tools: None are relevant to this analysis.

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