Is there evidence that some sites in the alignment have been subject to positive diversifying selection, either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)? In other words, BUSTED asks whether a given gene has been subject to positive, diversifying selection at any site, at any time. If a priori information about lineages of interest is available (e.g., due to migration, change in the environment, etc.), then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power.
BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection.
Note: the names of sequences in the alignment must match the names of the sequences in the tree.
A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
For each tested branch the analysis will infer the appropriate number of selective regimes, and whether or not there is statistical evidence of positive selection on that branch.
A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example)
--code Which genetic code to use
--branches Which branches should be tested for selection?
All [default] : test all branches
Internal : test only internal branches (suitable for
intra-host pathogen evolution for example, where terminal branches
may contain polymorphism data)
Leaves: test only terminal (leaf) branches
Unlabeled: if the Newick string is labeled using the {} notation,
test only branches without explicit labels
(see http://hyphy.org/tutorials/phylotree/)