R: Read Amino Acid Sequences in a File

read.aa {phangorn} | R Documentation

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

### See Also

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

[Package phangorn version 2.3.1 Index]