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.
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