R interface for gendist
This function is an R interface for gendist in the PHYLIP package (Felsenstein 2013). gendist can be used to estimate the evolutionary distances between populations based on gene frequency data. Three methods can be used for computing these distances. These are (1) Nei's genetic distance (Nei 1972), (2) Cavalli-Sforza's chord measure (Cavalli-Sforza & Edwards 1967), and (3) Reynolds et al.'s (1983) genetic distance.
either: (a) A matrix of allele frequencies (in columns) with rownames containing species names. In this case it is assumed that
path to the executable containing gendist. If
optional arguments to be passed to gendist. See details for more information.
Optional arguments include the following:
quiet suppress some output to R console (defaults to
quiet = FALSE);
method, the method for calculating the genetic distance - options are
"Reynolds" (defaults to
nalleles a vector containing the number of alleles per locus in
X (not used if
X is a list, and assumed to be a vector of
2s if ommitted); and
cleanup remove PHYLIP input & output files after the analysis is completed (defaults to
cleanup = TRUE).
More information about the gendist program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/gendist.html.
Obviously, use of any of the functions of this package requires that PHYLIP (Felsenstein 1989, 2013) should first be installed. Instructions for installing PHYLIP can be found on the PHYLIP webpage: http://evolution.genetics.washington.edu/phylip.html.
This function returns an object of class
Liam J. Revell, Scott A. Chamberlain
Maintainer: Liam J. Revell <firstname.lastname@example.org>
Cavalli-Sforza, L.L., Edwards, A.W.F. (1967) Phylogenetic analysis: models and estimation procedures. Evolution, 32, 550-570.
Felsenstein, J. (1989) PHYLIP–Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166.
Felsenstein, J. (2013) PHYLIP (Phylogeny Inference Package) version 3.695. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
Nei, M. (1972) Genetic distance between populations. American Naturalist, 106, 283-292.
Reynolds, J.B., Weir, B.S., Cockerham, C.C. (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics, 105, 767-779.
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