ClustalW-specific help
======================

msaClustalW offers the following parameters:

align=                       [Logical Value]
bootlabels=                  [String]
case=                        [String]
check=                       [Logical Value]
cluster=                     [String]
convert=                     [Logical Value]
dnamatrix=                   [Filename] or [String]
endgaps=                     [Logical Value]
fullhelp=                    [Logical Value]
gapdist=                     [Int]
gapOpening=                  [Numeric]
gapExtension=                [Numeric]
helixendin=                  [Int]
helixendout=                 [Int]
helixgap=                    [Int]
help=                        [Logical Value]
inputSeqs=                   [String]*, [Filename], or [XStringSet]
iteration=                   [String]
kimura=                      [Logical Value]
ktuple=                      [Int]
loopgap=                     [Int]
maxdiv=                      [Int]
maxiters=                    [Positive Int]
negative=                    [Logical Value]
nohgap=                      [Logical Value]
nopgap=                      [Logical Value]
nosecstr1=                   [Logical Value]
nosecstr2=                   [Logical Value]
novgap=                      [Logical Value]
noweights=                   [Logical Value]
options=                     [Logical Value]
order=                       [String]
output=                      [String]
outputtree=                  [String]
pairgap=                     [Int]
pim=                         [Logical Value]
profile=                     [Logical Value]
profile1=                    [Filename]
profile2=                    [Filename]
pwdnamatrix=                 [Filename] or [String]
pwgapext=                    [Numeric]
pwgapopen=                   [Numeric]
pwmatrix=                    [Filename] or [String]
quicktree=                   [Logical Value]
range=                       [Vector with 2 Positive Int]
score=                       [String]
secstrout=                   [String]
seed=                        [Int]
seqnos=                      [String]
seqno_range=                 [String]
sequences=                   [Logical Value]
stats=                       [Filename]
strandendin=                 [Int]
strandendout=                [Int]
strandgap=                   [Int]
substitutionMatrix=          [String]*, [Filename], or [Matrix]
terminalgap=                 [Int]
topdiags=                    [Int]
tossgaps=                    [Logical Value]
transweight=                 [Numeric]
tree=                        [Logical Value]
type=                        [String]
usetree=                     [Filename]
usetree1=                    [Filename]
usetree2=                    [Filename]
verbose=                     [Logical Value]
window=                      [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 "blosum" (see ?msaClustalW).

For more information on how these parameters are interpreted by
ClustalW, see http://www.clustal.org/download/clustalw_help.txt.
