read.aa {phangorn} | R Documentation |
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 rownames.
read.aa(file, format = "interleaved", skip = 0, nlines = 0, comment.char = "#", seq.names = NULL)
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 untill 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. |
a matrix of amino acid sequences.
Klaus Schliep k.p.schliep@massey.ac.nz
Anonymous. FASTA format description. http://www.ncbi.nlm.nih.gov/BLAST/fasta.html
Felsenstein, J. (1993) Phylip (Phylogeny Inference Package) version 3.5c. Department of Genetics, University of Washington. http://evolution.genetics.washington.edu/phylip/phylip.html
read.dna
, read.GenBank
,
phyDat
, read.alignment