Add one or more sequences to an existing multiple alignment that you wish to keep intact.
seq2aln(seq2add, aln, id = "seq", file = "aln.fa", ...)
a vector of sequence names to serve as sequence identifers.
name of ‘FASTA’ output file to which alignment should be written.
additional arguments passed to
This function calls the ‘MUSCLE’ program, to perform a profile profile alignment, which MUST BE INSTALLED on your system and in the search path for executables.
A list with two components:
an alignment character matrix with a row per sequence and a column per equivalent aminoacid/nucleotide.
sequence names as identifers.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
‘MUSCLE’ is the work of Edgar: Edgar (2004) Nuc. Acid. Res. 32, 1792--1797.
Full details of the ‘MUSCLE’ algorithm, along with download and
installation instructions can be obtained from:
A system call is made to the ‘MUSCLE’ program, which must be installed on your system and in the search path for executables.