RELAX: a test for selection differences

What question does this method answer?

Is there evidence the strength of selection has been relaxed (or conversely intensified) on a specified group of lineages (TEST) relative to a set of reference lineages (RELAX)? Importantly, RELAX is not designed to detect diversifying selection specifically. We note that the RELAX framework can perform both this specific hypothesis test as well as fit a suite of descriptive models which address, or example, overall rate differences between test and reference branches or lineage-specific inferences of selection relaxation.

Recommended Applications

1. Testing for a systematic shift (relaxation / intensification) in the distribution of selection pressure associated with major biological transitions such as hosting switching in viruses, lifestyle evolution in bacteria (i.e. transition from free-living to endosymbiotic lifestyle
2. Comparing selective regimes between two subsets of branches in the tree, e.g. to investigate selective differences due an environmental/phenotypic changes.

Brief description

RELAX (a random effects test of selection relaxation) uses a random effects branch-site model framework to test whether a set of 'Test' branches evolves under relaxed selection relative to a set of 'Reference' branches (R), as measured by the relaxation parameter (K).

Input

1. A FASTA sequence alignment.
2. A phylogenetic tree in the Newick format that is further partitioned into one or two groups (_TEST_ or _TEST_ and _REFERENCE_). See http://hyphy.org/tutorials/phylotree/

Note: the names of sequences in the alignment must match the names of the sequences in the tree.

Output

A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).

A custom visualization module for viewing these results is available (see http://vision.hyphy.org/RELAX for an example)

Further reading

http://hyphy.org/methods/selection-methods/#RELAX

Tool options

--code             Which genetic code to use

--model            Which type of test to run
                        All : fit 4 different models [default]
                        Minimal: only perform a 2-model test of relaxation/intensification  [faster]