ClustalOmega-specific help
==========================

msaClustalOmega offers the following parameters:

auto=                        [Logical Value]
clusteringOut=               [Filename]
cluster=                     [Positive Int]
dealign=                     [Logical Value]
distMatIn=                   [Filename]
distMatOut=                  [Filename]
force=                       [Logical Value]
full=                        [Logical Value]
fullIter=                    [Logical Value]
gapOpening=                  [Numeric] (currently not supported)
gapExtension=                [Numeric] (currently not supported)
guideTreeIn=                 [Filename]
guideTreeOut=                [Filename]
help=                        [Logical Value]
hmmIn=                       [Filename]
inFmt=                       [String]
inputSeqs=                   [String]*,[Filename], or [XStringSet]
isProfile=                   [Logical Value]
longVersion=                 [Logical Value]
macRam=                      [Int]
maxGuidetreeIterations=      [Int]
maxHmmIterations=            [Int]
maxiters=                    [Positive Int]
maxNumSeq=                   [Int]
maxSeqLen=                   [Int]
order=                       [String]
outfile=                     [Filename]
outFmt=                      [String]
percentId=                   [Logical Value]
profile1=                    [Filename]
profile2=                    [Filename]
residueNumber=               [Logical Value]
substitutionMatrix=          [String]*,[Filename], or [Matrix]
threads=                     [Positive Int]
type=                        [String]
useKimura=                   [Logical Value]
verbose=                     [Logical Value]
version=                     [Logical Value]
wrap=                        [Positive Int]

* The functionality for showing all available choices for string arguments
  is not available for the parameters inputSeqs and substitutionMatrix:
  - [String] in the context of inputSeqs means sequences supplied as
    a character vector.
  - [String] in the context of substitutionMatrix means a string, 
    which describes the matrix like "blosum30" (see ?msaClustalOmega).

For more information on how these parameters are interpreted by
ClustalOmega, see http://www.clustal.org/omega/README.
