MUSCLE-specific help
====================

msaMuscle offers the following parameters:

anchors=                     [Logical Value]
anchorspacing=               [Int]
brenner=                     [Logical Value]
center=                      [Negative Int]
cluster=                     [String]
cluster1=                    [String]
cluster2=                    [String]
core=                        [Logical Value]
diagbreak=                   [Positive Int]
diaglength=                  [Positive Int]
diagmargin=                  [Positive Int]
diags=                       [Logical Value]
diags1=                      [Logical Value]
diags2=                      [Logical Value]
dimer=                       [Logical Value]
distance1=                   [String]
distance2=                   [String]
gapOpening=                  [Numeric]
gapExtension=                [Numeric]
hydro=                       [Positive Int]
hydrofactor=                 [Positive Numeric]
in1=                         [Filename]
in2=                         [Filename]
inputSeqs=                   [String]*,[Filename], or [XStringSet]
le=                          [Logical Value]
maxhours=                    [Positive Numeric]
maxiters=                    [Positive Int]
maxtrees=                    [Positive Int]
minbestcolscore=             [Positive Numeric]
minsmoothscore=              [Positive Numeric]
noanchors=                   [Logical Value]
nocore=                      [Logical Value]
objscore=                    [String]
order=                       [String]
profile=                     [Logical Value]
refine=                      [Logical Value]
refinew=                     [Logical Value]
refinewindow=                [Positive Int]
root1=                       [String]
root2=                       [String]
smoothscoreceil=             [Numeric]
smoothwindow=                [Positive Int]
sp=                          [Logical Value]
spn=                         [Logical Value]
spscore=                     [Logical Value]
substitutionMatrix=          [Filename], or [Matrix]
SUEFF=                       [Positive Numeric] in Interval [0,1]
sv=                          [Logical Value]
type=                        [String]
version=                     [Logical Value]

* The functionality for showing all available choices for string arguments
  is not available for the parameter inputSeqs:
- [String] in the context of inputSeqs means sequences supplied as
  a character vector.

For more information on how these parameters are interpreted by
MUSCLE, see http://www.drive5.com/muscle/muscle.html.

