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distmate - Online in the Cloud

Run distmate in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command distmate that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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