dartR.base (version 1.0.5)

gl.tree.fitch: Generates a distance phylogeny

Description

Generates a distance phylogeny from a distance object using the Fitch-Margoliash algorithm in Phylip.

Usage

gl.tree.fitch(
  D,
  x = NULL,
  phylip.path,
  out.path = tempdir(),
  tree.method = "FM",
  outgroup = NULL,
  global.rearrange = FALSE,
  randomize = FALSE,
  n.jumble = 9,
  bstrap = 1,
  plot.type = "phylogram",
  bstrap.threshold = 0.8,
  branch.width = 2,
  branch.color = "blue",
  node.label.color = "red",
  terminal.label.cex = 0.8,
  node.label.cex = 0.8,
  offset = 1.2,
  verbose = NULL
)

Value

The tree file in newick format.

Arguments

D

Name of the distance matrix for tree building [required]

x

Name of the genlight object containing the SNP data [required for bootstrapping, default NULL].

phylip.path

Path to the directory that holds the Phylip executables [required].

out.path

Path to the directory to save files produced by the analysis [default tempdir()]

tree.method

Algorithm used for constructing trees and selecting the best tree [default "FM"]

outgroup

Name of the outgroup taxon [default NULL, no outgroup, tree not rooted]

global.rearrange

If TRUE, undertake global rearrangements when generating the tree [default FALSE].

randomize

If TRUE, randomize the order of the input taxa [default FALSE].

n.jumble

Number of randomizations of the input order, must be odd [default 9]

bstrap

Number of bootstrap replicates [default 1000]

plot.type

One of 'phylogram','cladogram','unrooted','fan','tidy','radial' [default "phylogram"]

bstrap.threshold

Threshold for bootstrap values to be displayed on the tree [default 0.8]

branch.width

Width of the branches [default 2]

branch.color

Colour of the branches [default "blue"]

node.label.color

Colour of the node labels [default "red"]

terminal.label.cex

Height of the taxon label text [default 0.8]

node.label.cex

Height of the node label text [default 0.8]

offset

Horizontal offset of the node labels from the node [default 1.8]

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Author

Custodian: Arthur Georges -- Post to https://groups.google.com/d/forum/dartr

Details

The script takes a distance object as input. This distance object is typically created with gl.dist.phylo(). The script then creates a file consistent with what is expected by program fitch in the Phylip suite of executables. It then runs fitch to generate the "best" phylogenetic tree. Program fitch is run again with bstrap replicates to generate bootstrap support for each node in the tree and plots these on the tree.

tree.method : Currently only Fitch-Margoliash is implemented.

outgroup : Name the taxon to be used as outgroup. Must be among the names of the populations defined in the genlight object.

See Also

Other phylogeny: gl.dist.phylo()

Examples

if (FALSE) {
tmp <- gl.filter.monomorphs(testset.gl)
D <- gl.dist.phylo(testset.gl,subst.model="F81")
gl.phylip(D=D,x=tmp,phylip.path="D:/workspace/R/phylip-3.695/exe",plot.type="unrooted",
node.label.cex=0.5,terminal.label.cex=0.6,global.rearrange = FALSE, bstrap=10)
}