R: Import and export sequence alignments

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 `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` retuns 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")

[Package phangorn version 2.6.2 Index]