Policy Document


Copyright (C) 1996-97 Nick Ross. This documentation by B.G. Spratt and Nick Ross.

  To download Sequence Output CLICK HERE

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 or informative
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
reading frames.

- The program provides considerable control over the numbering of the
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 sequences",
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 Winzip.