NAME

       distmat - Create a distance matrix from a multiple sequence alignment

SYNOPSIS

       distmat -sequence seqset -nucmethod list -protmethod list -ambiguous boolean -gapweight float
               -position integer -calculatea boolean -parametera float -outfile outfile

       distmat -help

DESCRIPTION

       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).

OPTIONS

   Input section
       -sequence seqset
           File containing a sequence alignment.

   Required section
       -nucmethod list
           Multiple substitution correction methods for nucleotides.

       -protmethod list
           Multiple substitution correction methods for proteins.

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

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

       -position integer
           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

       -calculatea boolean
           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

       -parametera float
           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

   Output section
       -outfile outfile

BUGS

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to
       the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

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

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be
       redistributed under the same terms as EMBOSS itself.

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