msaMuscle {msa} | R Documentation |
This function calls the multiple sequence alignment algorithm MUSCLE.
msaMuscle(inputSeqs, cluster="default", gapOpening="default", gapExtension="default", maxiters="default", substitutionMatrix="default", type="default", order=c("aligned", "input"), verbose=FALSE, help=FALSE, ...)
inputSeqs |
input sequences; see |
cluster |
The clustering method which should be used.
Possible values are |
gapOpening |
gap opening penalty; the default
is 400 for DNA sequences and 420 for RNA sequences. The default
for amino acid sequences depends on the profile score settings:
for the setting |
gapExtension |
gap extension penalty; the default is 0. |
maxiters |
maximum number of iterations; the default is 16.
In the original MUSCLE implementation, it is also possible
to set |
substitutionMatrix |
substitution matrix for scoring matches and
mismatches; can be a real matrix or a file name
If the file interface is used, matrices have to be in NCBI-format.
The original MUSCLE implementation also accepts matrices in WU_BLAST
(AB_BLAST) format, but, due to copyright restrictions,
this format is not supported by |
type |
type of the input sequences |
order |
how the sequences should be ordered in the output object
(see |
verbose |
if |
help |
if |
... |
further parameters specific to MUSCLE;
An overview of parameters that are available in this interface
is shown when calling |
This is a function providing the MUSCLE multiple alignment
algorithm as an R function. It can be used for various types of
sequence data (see inputSeqs
argument above). Parameters that
are common to all multiple sequences alignments provided by the
msa package are explicitly provided by the function and named
in the same for all algorithms. Most other parameters that are
specific to MUSCLE can be passed to MUSCLE via additional
arguments (see argument help
above).
For a note on the order of output sequences and direct reading from
FASTA files, see msa
.
Depending on the type of sequences for which it was called,
msaMuscle
returns a MsaAAMultipleAlignment
,
MsaDNAMultipleAlignment
, or
MsaRNAMultipleAlignment
object.
If called with help=TRUE
, msaMuscle
returns
an invisible NULL
.
Enrico Bonatesta and Christoph Horejs-Kainrath <msa@bioinf.jku.at>
http://www.bioinf.jku.at/software/msa
U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015). msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997-3999. DOI: 10.1093/bioinformatics/btv494.
http://www.drive5.com/muscle/muscle.html
Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797. DOI: 10.1093/nar/gkh340.
Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. DOI: 10.1186/1471-2105-5-113.
msa
, MsaAAMultipleAlignment
,
MsaDNAMultipleAlignment
,
MsaRNAMultipleAlignment
,
MsaMetaData
## read sequences filepath <- system.file("examples", "exampleAA.fasta", package="msa") mySeqs <- readAAStringSet(filepath) ## call msaMuscle with default values msaMuscle(mySeqs) ## call msaMuscle with custom parameters msaMuscle(mySeqs, gapOpening=12, gapExtension=3, maxiters=16, cluster="upgmamax", SUEFF=0.4, brenner=FALSE, order="input", verbose=FALSE) ## call msaMuscle with a custom substitution matrix data(PAM120) msaMuscle(mySeqs, substitutionMatrix=PAM120)