# R interface for seqboot

### Description

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).

### Usage

1 |

### Arguments

`X` |
either: (a) an object of class |

`path` |
path to the executable containing seqboot. If |

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

### Details

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.

### Value

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.

### Author(s)

Liam J. Revell, Scott A. Chamberlain

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

### References

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

Felsenstein, J. (1989) PHYLIPâ€“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.