DISTMAT(1e) | EMBOSS Manual for Debian | DISTMAT(1e) |
NAME¶
distmat - Create a distance matrix from a multiple sequence alignmentSYNOPSIS¶
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 seqsetFile containing a sequence alignment.
Required section¶
-nucmethod listMultiple substitution correction methods for
nucleotides.
-protmethod list
Multiple substitution correction methods for
proteins.
Additional section¶
-ambiguous booleanOption 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 outfileBUGS¶
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.
05/11/2012 | EMBOSS 6.4.0 |