Order is a program designed to be run interactively. Its functions are to process the output of a MULTALIGN in pairwise mode and produce the following files.
Type order.
NGAPS(1) (Use the number of gaps - totally useless) PIDENT(2) Use percentage identities - possibly useful. NAS(3) Normalised alignment score (see description of Multalign pairwise mode for explanation) NASAL(4) As for NAS RSCORE(5) Use S.D. scores calculated from randomizations.
Answer with an integer 1-5 (Usually 3 or 5) 5 is best if you've calculated it.
(This is followed by a request for plotting details - note, there is a bug in the programme, you MUST supply a title and axis title, but these won't appear on the output - The page width requested, refers to the number of plotting characters typically 80 or 132).