distmat - Create a distance matrix from a multiple sequence alignment

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EMBOSS 6.4.0                                       05/11/2012                                        DISTMAT(1e)

distmat is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It
       is part of the "Phylogeny:Molecular sequence" command group(s).

       distmat - Create a distance matrix from a multiple sequence alignment

Inputsection-sequenceseqset
           File containing a sequence alignment.

   Requiredsection-nucmethodlist
           Multiple substitution correction methods for nucleotides.

       -protmethodlist
           Multiple substitution correction methods for proteins.

   Additionalsection-ambiguousboolean
           Option to use the ambiguous codes in the calculation of the Jukes-Cantor method or if the sequences
           are proteins. Default value: N

       -gapweightfloat
           Option to weight gaps in the uncorrected (nucleotide) and Jukes-Cantor distance methods. Default
           value: 0.

       -positioninteger
           Choose base positions to analyse in each codon i.e. 123 (all bases), 12 (the first two bases), 1, 2,
           or 3 individual bases. Default value: 123

       -calculateaboolean
           This will force the calculation of parameter 'a' in the Jin-Nei Gamma distance calculation, otherwise
           the default is 1.0 (see -parametera option). Default value: N

       -parameterafloat
           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. Default value: 1.0

   Outputsection-outfileoutfile

       distmat is fully documented via the tfm(1) system.

distmat-sequenceseqset-nucmethodlist-protmethodlist-ambiguousboolean-gapweightfloat-positioninteger-calculateaboolean-parameterafloat-outfileoutfiledistmat-help