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HyPhy-SLAC (version 2.5.47+galaxy0)
If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree

SLAC : Single Likelihood Ancestor Counting

What question does this method answer?

Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, diversifying selection?

Brief description

SLAC (Single Likelihood Ancestor Counting) uses a maximum likelihood ancestral state reconstruction and minimum path substitution counting to estimate site - level dS and dN, and applies a simple binomial - based test to test if dS differs drom dN. The estimates aggregate information over all branches, so the signal is derived from pervasive diversification or conservation. A subset of branches can be selected for testing as well.

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).

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

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/)

 --pvalue           The significance level used to determine significance

 --samples          Draw this many alternative ancestral state reconstructions
                    to evaluate uncertainty