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  HyPhy Documentation: Standard Analyses: RelativeRatio.bf

      Summary: Given 2 nucleotide, aminoacid or codon data files with the same number of sequences, a tree, and a relevant substitution model, RelativeRatio calculates two sets of MLE:

  • Unconstrained Model : all model parameters (rates) for each data file are estimated independently. This is the alternative hypothesis. 
  • Ratio Constrained Model : rates in the second data set are assumed to be proportional to rates in the first one. This is the null hypothesis. 
A likelihood ratio test is then performed to determine whether the alternative hypothesis should be accepted or rejected.

     Input: Two nucleotide, aminoacid or codon data files 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. A Newick style tree string can either be included in the first data file, or supplied via a separate tree files. Note, that if a data file contains more than one tree, only the first one will be read. The second file should contain at least as many sequences as the first one; if it contains more sequences, then only as many as there are in the first file will be used.

    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: The standard output depends on the "Likelihood Output" option selected in "Preferences". By default, that option is to print the maximum ln-likelihood followed by a tree string with branch lengths representing the expected number of substitutions per codon. For a complete list of output options, refer the Output Formats page. The analysis will report MLE for the unconstrained model (null hypothesis), ratio constrained model (alternative hypothesis) and the likelihood ratio test. The latter includes the value of the likelihood ratio statistic and the P-Value based on the fact that LR statistic is asymptotically distributed as Chi-squared with degrees of freedom equal to the number of constrained model parameters (that number varies based on the model chosen).

     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. "lf1" is the unconstrained likelihood function for the first data set, "lf2" is the unconstrained likelihood function for the second data set, and "lfConstrained" is the joint likelihood function with ratio constraints in place.

      Bootstrapping tools output a summary of simulations on the screen for unconstrained and constrained MLE (mean and variance), the same descriptors for the ratio parameter R, and the likelihood statistic sample distribution, including mean, variance and simulated P-Value (proportion of simulated LR which is larger than the original LR). They also save LR for each data replicate in a comma-separated file suitable for import by data processing programs. 

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