read.phyDat: Import and export sequence alignments

In phangorn: Phylogenetic Reconstruction and Analysis

Import and export sequence alignments

Description

These functions read and write sequence alignments.

Usage

read.phyDat(file, format = "phylip", type = "DNA", ...)

write.phyDat(x, file, format = "phylip", colsep = "", nbcol = -1, ...)

Arguments

file	a file name specified by either a variable of mode character, or a double-quoted string.
format	File format of the sequence alignment (see details). Several popular formats are supported: "phylip", "interleaved", "sequential", "clustal", "fasta" or "nexus", or any unambiguous abbreviation of these.
type	Type of sequences ("DNA", "AA", "CODON" or "USER").
...	further arguments passed to or from other methods.
x	An object of class phyDat.
colsep	a character used to separate the columns (a single space by default).
nbcol	a numeric specifying the number of columns per row (-1 by default); may be negative implying that the nucleotides are printed on a single line.

Details

write.phyDat calls the function write.dna or write.nexus.data and read.phyDat calls the function read.dna, read.aa or read.nexus.data, so see for more details over there.

You may import data directly with read.dna or read.nexus.data and convert the data to class phyDat.

Value

read.phyDat returns an object of class phyDat, write.phyDat write an alignment to a file.

Author(s)

Klaus Schliep [e-mail]

References

https://www.ncbi.nlm.nih.gov/blast/fasta.shtml Felsenstein, J. (1993) Phylip (Phylogeny Inference Package) version 3.5c. Department of Genetics, University of Washington. https://evolution.genetics.washington.edu/phylip/phylip.html

See Also

read.dna, read.GenBank, phyDat, read.alignment

Examples

fdir <- system.file("extdata/trees", package = "phangorn")
primates <- read.phyDat(file.path(fdir, "primates.dna"),
                        format = "interleaved")

phangorn documentation built on Jan. 23, 2023, 5:37 p.m.