Multiple alignment
Quickly computing a smallish multiple sequence alignment.
msalign(fsa.tbl, machine = "microseq::muscle")
fsa.tbl |
A fasta object ( |
machine |
Function that does the 'dirty work'. |
This function computes a multiple sequence alignment given a set of sequences in
a fasta object, see readFasta for more on fasta objects.
It is merely a wrapper for the function named in machine to avoid explicit writing
and reading of files. This function should only be used for small data sets, since no result
files are stored. For heavier jobs, use the machine function directly.
At present, the only machine function implemented is muscle, but other
third-party machines may be included later.
Note that this function will run muscle with default settings, which is fine
for small data sets.
Results are returned as a fasta object, i.e. a tibble with columns
Header and Sequence.
Lars Snipen.
## Not run:
prot.file <- file.path(file.path(path.package("microseq"),"extdata"),"small.faa")
faa <- readFasta(prot.file)
msa <- msalign(faa)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.