Does evolution at specific sites in a coding alignment preserve or alter some biochemical properties?
Identify biochemical evolutionary constraints or changes with site level resolution: e.g. site 23 is evolving to conserve residue polarity, but alter it's volume.
Most methods of coding sequence analysis do not take direct account of the fact that the rate at which amino-acids are exchanged is different depending on the amino-acids. While this seems obvious (e.g. radical changes should happen slower), there are many technical reasons for why the standard assumption of "one-rate for all residues" holds.
Given a set of N amino-acid properties, fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...). When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted. At each site, N+1 tests are performed (one for each property, and an omnibus test).
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).
A custom visualization module for viewing these results will soon be available at http://vision.hyphy.org/
--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
--properties Which property set to use
Atchley : Use the five properties derived from a factor analysis of 500 amino-acid properties [Table 2 in PNAS (2005) 102(18) 6395-6400 doi: 10.1073/pnas.0408677102]
LCAP: Use the five properties defined in the Conant and Stadler LCAP model [Mol Biol Evol (2009) 26 (5): 1155-1161. doi: 10.1093/molbev/msp031]