genewarpi: Aligns two gene expression time series (interpolative time warping).
  program version = 1.0 (20000814-14:30:20)
Supported parameters:

-D (write algorithm data?)
  If not supplied, algorithm data not written to "-d" data
    file, suppressing the ability to generate graphics for the alignment.

  syntax: -D (boolean switch);  Not required; Default = on.

-a (algorithm)
  Algorithm employed for time alignment.  "1" = time weights applied to 
    right endpoint distances of aligned consecutive time point pairs.  "2"
    = time weights applied to averages of distances of left and right
    endpoints.

  syntax: -a pos-integer;  Not required; Default = 2.

-d (output data file)
  File used to pass data to graphics generation system.
    Default is output message file name + ".data" if
    not provided.  Suppressed by "-~D" parameter.

  syntax: -d string;  Not required; No default.

-debug (produce debugging messages)
  Causes system debug messages to be printed.

  syntax: -debug (boolean switch);  Not required; Default = off.

-enforceorder (enforce time order)
  Interpolative alignment can result in interpolative time points being
    aligned out of order.  When specified, this parameter will force 
    time points to be in order at the cost of producing a possibly sub-optimal
    alignment.

  syntax: -enforceorder (boolean switch);  Not required; Default = off.

-i1 (input file name 1)
  First of two time series files being synchronized.
  Time series file format is:
    >N|seriesname| description\n
    time-1  time-2  .... time-k\n
    genename-1 \t data-1 data-2 .... data-k\n
      ... ... ... ... 
    genename-m \t data-1 data-2 .... data-k\n
  Times must be in order.

  syntax: -i1 string;  Required; No default.

-i2 (input file name 2)
  Second of two time series files being synchronized.
   Must contain same gene names as in "-i1" file.

  syntax: -i2 string;  Required; No default.

-intprec (interpolation precision)
  Precision of reported interpolation values.

  syntax: -intprec non-neg-integer;  Not required; Default = 3.

-np (max number optimal paths)
  Maximum number of optimal time alignments that will be reported.

  syntax: -np pos-integer;  Not required; Default = 10.

-o (output file name)
  Output message file; STDOUT if not specified.

  syntax: -o string;  Required; No default.

-p (parameter file name)
  Allows parameters to be provided in file.

  syntax: -p string;  Not required; No default.

-pathopt (path options)
  Optimal path computation and reporting options.
    0 = Do not compute or report paths.
    1 = Compute and report (unreduced) optimal paths.
    2 = Compute and report reduced optimal paths.
    3 = Compute and report both reduced and unreduced optimal paths.
    Optimal paths are composed of nodes of the form ((i,r),j) and
    (i,(j,r)), where i and j are time point indices in the input
    time series and 0 <= r <= 1 is an interpolation fraction.
    Reduced optimal paths are optimal paths reported as (i+r,j)
    and (i,j+r) where duplicate nodes have been eliminated.
    (An example of duplicate nodes would be ((2,1),4) -> (3,(4,0)).)
    Suppressing path computation with -pathopt 0 affects score and
    path interpolation order error checking.

  syntax: -pathopt non-neg-integer;  Not required; Default = 2.

-f... (feature weight for ...)
  Weight applied to specified feature in algorithm distance calculations.
      Name specified by ... must match feature name in input files ("-i1"       and "-i2").
  syntax: -f... non-negative number; Not required; Default = 1.0.