User Guide to the program ORDER

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.

1. Order_file.
2. tree_file/order_file. (cluster analysis)
3. graphical output - a simple dendrogram is produced.

Type order.

1. The program will then ask you for the name of a file produced by MULTALIGN in pairwise mode ( but not including any alignments).

2. Does the input file have timings? If you specified pairwise_timer= when running MUTALIGN then answer Yes, otherwise N (Default=N).

3. Enter filename for comparisons to exclude - press <return>.

4. Options: Five possible results of pairwise comparison may be used to perform the ordering or cluster analysis.

   
   
    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.

5. Produce an order file? [Y] Answering Yes to this option prompts for a filename, then exits the program. The order is defined in a manner suitable for the single order multiple alignment algorithm.

6. Answering No to 5. gives the question Perform cluster analysis ? [Y] Answer Yes then you get
   1. Save full cluster details? (ie do we want to generate a tree_fileand a compatible order_filefor subsequent use by MULTALIGN to perform tree based multiple alignment?? The default is YES. If we answer Yes, then we are next prompted for an order filename and tree filename to be written.

      (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).

7. Answering No to 6. gives the question 'Give ADDTREE filename' This allows the pairwise scores to be written out in a form that can be read by the cluster analysis program ADDTREE (See Corter(1982))