phangorn: read.aa – R documentation

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read.aa

Read Amino Acid Sequences in a File

Description

This function reads amino acid sequences in a file, and returns a matrix list of DNA sequences with the names of the taxa read in the file as row names.

Usage

read.aa(file, format = "interleaved", skip = 0, nlines = 0,
  comment.char = "#", seq.names = NULL)

Arguments

`file`	a file name specified by either a variable of mode character, or a double-quoted string.
`format`	a character string specifying the format of the DNA sequences. Three choices are possible: `"interleaved"`, `"sequential"`, or `"fasta"`, or any unambiguous abbreviation of these.
`skip`	the number of lines of the input file to skip before beginning to read data.
`nlines`	the number of lines to be read (by default the file is read until its end).
`comment.char`	a single character, the remaining of the line after this character is ignored.
`seq.names`	the names to give to each sequence; by default the names read in the file are used.

Value

a matrix of amino acid sequences.

Author(s)

Klaus Schliep klaus.schliep@gmail.com

References

https://en.wikipedia.org/wiki/FASTA_format

Felsenstein, J. (1993) Phylip (Phylogeny Inference Package) version 3.5c. Department of Genetics, University of Washington. https://evolution.genetics.washington.edu/phylip/phylip.html