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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