writeDist: Writing and reading distances in phylip and nexus format

In phangorn: Phylogenetic Reconstruction and Analysis

Writing and reading distances in phylip and nexus format

Description

readDist, writeDist and write.nexus.dist are useful to exchange distance matrices with other phylogenetic programs.

Usage

writeDist(x, file = "", format = "phylip", ...)

write.nexus.dist(x, file = "", append = FALSE, upper = FALSE,
  diag = TRUE, digits = getOption("digits"), taxa = !append)

readDist(file, format = "phylip")

read.nexus.dist(file)

## S3 method for class 'dist'
unique(x, incomparables, ...)

Arguments

x	A dist object.
file	A file name.
format	file format, default is "phylip", only other option so far is "nexus".
...	Further arguments passed to or from other methods.
append	logical. If TRUE the nexus blocks will be added to a file.
upper	logical value indicating whether the upper triangle of the distance matrix should be printed.
diag	logical value indicating whether the diagonal of the distance matrix should be printed.
digits	passed to format inside of write.nexus.dist.
taxa	logical. If TRUE a taxa block is added.
incomparables	Not used so far.

Value

an object of class dist

Author(s)

Klaus Schliep [e-mail]

References

Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an extensible file format for systematic information. Systematic Biology, 46, 590–621.

See Also

To compute distance matrices see dist.ml dist.dna and dist.p for pairwise polymorphism p-distances

Examples

data(yeast)
dm <- dist.ml(yeast)
writeDist(dm)
write.nexus.dist(dm)

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.