SEQUENCE OUTPUT - Windows DOS exe.
Copyright (C) 1996-97 Nick Ross. This documentation by B.G.
Spratt and Nick Ross.
The Purpose of Sequence Output -
- The program is useful when DNA sequence has been obtained
from the same
gene from multiple isolates/strains/species. It can list out
a "master" sequence, and
show the positions where the other sequences differ. The sequence
used as the master,
and the order the sequences are listed, is controlled by the
order in which you enter
them when you run the program.
- You can list just the nucleotide differences, or just the
amino acid differences, or
both. You can also list only the variable (polymorphic) nucleotide
sites, or only the
informative nucleotide sites, or just the subset of the polymorphic
nucleotide sites that are "silent". You can also
list only the variable amino acid
- There is also the option to translate a single nucleotide
sequence in all six
- The program provides considerable control over the numbering
nucleotide/amino acid sites in the output.
- Note that you need to know the reading frame to use the
amino acids only, or
the nucleotides plus amino acids option. The safest option
is to make sure that
nucleotide 1 in the sequence file is the first position of
a codon. Of course, you also
need to make sure that the reading frame is correct when you
choose to output silent
nucleotide sites, informative nucleotide sites, variable amino
acid residues etc.
- Sequence Output is able to examine all current sequences
and identify all alleles
present. It is then possible to generate OTUs that have the
names "allele1", "allele2",
etc. corresponding to the alleles identified. Each time this
option is chosen the program
groups the new OTUs, if they have been generated, as the "previous
facilitating the creation of new MEGA/PHYLIP files (see later)
that only contain one
instance of each allele.
Full instructions are included in the download - You will
need a decompression programme to open the package such as