distmat1e
Create a distance matrix from a multiple sequence alignment
Usage
distmat -sequence
seqset
-nucmethod
list
-protmethod
list
-ambiguous
boolean
-gapweight
float
-position
integer
-calculatea
boolean
-parametera
float
-outfile
outfile
distmat -help
Overview
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
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.