Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqset     File containing a sequence alignment.
*  -nucmethod          menu       [0] Multiple substitution correction methods
                                  for nucleotides. (Values: 0 (Uncorrected);
                                  1 (Jukes-Cantor); 2 (Kimura); 3 (Tamura); 4
                                  (Tajima-Nei); 5 (Jin-Nei Gamma))
*  -protmethod         menu       [0] Multiple substitution correction methods
                                  for proteins. (Values: 0 (Uncorrected); 1
                                  (Jukes-Cantor); 2 (Kimura Protein))
  [-outfile]           outfile    [*.distmat] Phylip distance matrix output
                                  file

   Additional (Optional) qualifiers (* if not always prompted):
*  -ambiguous          boolean    [N] Option to use the ambiguous codes in the
                                  calculation of the Jukes-Cantor method or
                                  if the sequences are proteins.
*  -gapweight          float      [0.] Option to weight gaps in the
                                  uncorrected (nucleotide) and Jukes-Cantor
                                  distance methods. (Any numeric value)
*  -position           integer    [123] Choose base positions to analyse in
                                  each codon i.e. 123 (all bases), 12 (the
                                  first two bases), 1, 2, or 3 individual
                                  bases. (Any integer value)
*  -calculatea         boolean    [N] This will force the calculation of
                                  parameter 'a' in the Jin-Nei Gamma distance
                                  calculation, otherwise the default is 1.0
                                  (see -parametera option).
*  -parametera         float      [1.0] User defined parameter 'a' to be use
                                  in the Jin-Nei Gamma distance calculation.
                                  The suggested value to be used is 1.0 (Jin
                                  et al.) and this is the default. (Any
                                  numeric value)

   Advanced (Unprompted) qualifiers: (none)
   General qualifiers:
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose