| read.phyDat {phangorn} | R Documentation |
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 |
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 klaus.schliep@gmail.com
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")