Read Amino Acid Sequences in a File
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.
read.aa(file, format = "interleaved", skip = 0, nlines = 0, comment.char = "#", seq.names = NULL)
a file name specified by either a variable of mode character, or a double-quoted string.
a character string specifying the format of the DNA sequences. Three choices are possible:
"fasta", or any unambiguous abbreviation of these.
the number of lines of the input file to skip before beginning to read data.
the number of lines to be read (by default the file is read until its end).
a single character, the remaining of the line after this character is ignored.
the names to give to each sequence; by default the names read in the file are used.
a matrix of amino acid sequences.
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