Rgendist(X, path=NULL, ...)m - 1 allele frequencies are reported for a locus with m segregating alleles. (The mth frequency is just one minus the sum of the other m-1.) Or (b) a list of matrices in which each row contains the relative frequency of alleles at a locus for a species. In this case, the rownames of each matrix in the list should contain the species names. Here the number of alleles at each locus can be inferred from the number of columns in the matrix, and no frequencies should be omitted. (I.e., rows should add to 1.0.)path = NULL, the R will search several paths for gendist. See details for more information."dist".
quiet suppress some output to R console (defaults to quiet = FALSE); method, the method for calculating the genetic distance - options are "Nei", "Cavalli-Sforza", and "Reynolds" (defaults to method="Nei"); 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.
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.
Rdnadist, Rprotdist