Import and export sequence alignments

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.

Value

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

Details

write.phyDat calls the function write.dna or write.nexus.data and read.phyDat calls the function read.dna 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.

References

Anonymous. FASTA format description. 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://phylipweb.github.io/phylip/

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

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