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
distmat - Create a distance matrix from a multiple sequence alignment
distmat -sequence seqset -nucmethod list -protmethod list -ambiguous boolean
-gapweight float -position integer -calculatea boolean -parametera float
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).
File containing a sequence alignment.
Multiple substitution correction methods for nucleotides.
Multiple substitution correction methods for proteins.
Option to use the ambiguous codes in the calculation of the Jukes-Cantor method or if
the sequences are proteins. Default value: N
Option to weight gaps in the uncorrected (nucleotide) and Jukes-Cantor distance
methods. Default value: 0.
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
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
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:
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