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HyPhy-FEL (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
Allow synonymous rates to vary from site to site
Warning: This will result in a significantly slower analysis. This parameter specifies the maximum number of replicates per site.

FEL : Fixed effects likelihood

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

FEL (Fixed Effects Likelihood) estimates site-wise synonymous (alpha) and non-synonymous rates (beta), and uses a likelihood ratio test to determine if beta != alpha at a site. 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, in which case an additional (nuisance) parameter will be inferred -- the non-synonymous rate on branches NOT selected for testing.


  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.


A JSON file with analysis results ( A custom visualization module for viewing these results is available (see 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

 --pvalue           The significance level used to determine significance

 --srv              Include site-to-site synonymous rate variation?
                        Yes [default] or No