aBSREL : Adaptive Branch-Site Random Effects Likelihood

What question does this method answer?

Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny?

Recommended Applications

1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences).
2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences)

Brief description

aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch.

Input

1. A FASTA sequence alignment.
2. A phylogenetic tree in the Newick format

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).

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/aBSREL for an example)

Further reading

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

Tool options

--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/)