Add one or more sequences to an existing multiple alignment that you
wish to keep intact.
Usage
seq2aln(seq2add, aln, id = "seq", file = "aln.fa", ...)
Value
A list with two components:
ali
an alignment character matrix with a row per sequence and
a column per equivalent aminoacid/nucleotide.
id
sequence names as identifers.
Arguments
seq2add
an sequence character vector or an alignment list
object with id and ali components, similar to that
generated by read.fasta and seqaln.
aln
an alignment list object with id and ali
components, similar to that generated by read.fasta
and seqaln.
id
a vector of sequence names to serve as sequence
identifers.
file
name of ‘FASTA’ output file to which alignment
should be written.
...
additional arguments passed to seqaln.
Author
Barry Grant
Details
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.
References
Grant, B.J. et al. (2006) Bioinformatics22, 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: http://www.drive5.com/muscle/.