genewarp: Aligns two gene expression time series (simple time warping).
  program version = 1.0 (20000814-14:21:15)
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.

-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.

-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.

-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.