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. |