R interface for seqboot


This function is an R interface for seqboot in the PHYLIP package (Felsenstein 2013). seqboot can be to perform the non-parametric bootstrap following Felsenstein (1985).


Rseqboot(X, path=NULL, ...)



either: (a) an object of class "DNAbin" containing DNA sequences or an object of class "proseq" containing amino acid sequences; (b) an object of class "phylip.data" containing data for a binary or multi-state discrete character; (c) an object of class "rest.data" containing restriction site data; or (d) a matrix with gene frequency data (this option does not presently work properly).


path to the executable containing seqboot. If path = NULL, the R will search several paths for seqboot. See details for more information.


optional arguments to be passed to seqboot. See details for more information.


Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); type the data type (options are "sequence", "morph", "rest", or "gene.freq"); method analysis method (options are "bootstrap", "jacknife", and "permute"); percentage a bootstrap or jacknife percentage (can be >100); block.size block size in number of characters for the bootstrap, jacknife, or permutation (defaults to 1, the regular bootstrap); replicates number of replicates (defaults to 100); weights a vector of weights that must be 0 or 1 - characters with weight of 0 are excluded from the resampling procedure; rate.categories vector of integers between 1 and 9 indicating the rate category for each character - this is supplied so that resampled rate categories can be output by the method; mixture vector of "W" and "C" (see Rmix); and cleanup remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE).

More information about the seqboot program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/seqboot.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 a list of objects of class "DNAbin", "proseq", "phylip.data", or "rest.data" depending on the input data type. If ancestors, mixture, or rate.categories are supplied, then each element of the list contains an object data (containing the data), and vectors ancestors, mixture, and/or categories, containing the resampled input vectors.


Liam J. Revell, Scott A. Chamberlain

Maintainer: Liam J. Revell <liam.revell@umb.edu>


Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.

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.

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker. Vote for new features on Trello.

comments powered by Disqus