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).

* ClustalOmega crashes if profile1 is used in conjunction with a non-default
  output order. That is why the order argument is ignored when profile1 is
  specified. (a warning is also displayed in this case)

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