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  HyPhy Documentation: Standard Analyses: RelativeRate.bf

      Summary: Given 3 nucleotide, aminoacid or codon sequences and a relevant substitution model, RelativeRate 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.

     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. If the file contains less than 3 sequences HYPHY will prompt the user to select additional sequence file(s), which should contain sequences of the same type and length. If the file contains more than 3 sequences, HYPHY will prompt the user to choose three of them for the analysis. The user also selects which sequence will be the outgroup. 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: 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), rate 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. "lf" is the unconstrained likelihood function and "lfConstrained" is the one with rate constraints in place.

      Bootstrapping tools output a summary of simulations on the screen for unconstrained and constrained MLE (mean and variance) 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 detailed MLE and 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