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.
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://phylipweb.github.io/phylip/
Author
Klaus Schliep klaus.schliep@gmail.com