calc.Dss.syn: Calculate the Dss statistic using synonymous distances
In synDss: Recombination detection using synonymous distances

Description Usage Arguments Details Value Author(s) References See Also

This function calculates the Dss statistic using sliding windows and synonymous distance

1	calc.Dss.syn(data, l, m, syn.matrix, exhaustive=FALSE)

`data`	The sequence alignment, as a matrix of A,C,T,G characters
`l`	Step size for the sliding windows
`m`	Half-window size (total window size will be 2m)
`syn.matrix`	An indicator matrix which specifies the transitions of interest. For synonymous distances, each entry will be a 1 for synonymous changes, and 0 for non-synonymous changes. See `regist.synonym`.
`exhaustive`	logical; if TRUE, an exhaustive search over all possible topologies is performed at each step.

Unless exhaustive=TRUE, this function uses bionj to quickly obtain the neighbor-joining tree before finding optimal branch lengths using least squares for each half-window; the branch length estimation is restricted to the topology obtained by the neighbor-joining algorithm.

A vector of numeric values, representing the Dss statistic at each window location.

Peter Chi pchi@calpoly.edu

G. McGuire, F. Wright, and M.J. Prentice. A graphical method for detecting recombination in phylogenetic data sets. Molecular Biology and Evolution, 14:1125-1131, 1997.

N. Saitou and M. Nei. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4:406-425, 1987.

J.D. O'Brien, V.N. Minin, and M.A. Suchard. Learning to count: robust estimates for labeled distances between molecular sequences. Molecular Biology and Evolution, 26:801-814, 2009.

calc.Dss

synDss documentation built on May 2, 2019, 5:40 p.m.