gcg2 17% ls
best.pair             capb_human.sw         k02938.gb_ov
capb.txt              capb_mouse.sw         pileup.figure
capb_caeel.swissprot  fetch.msf             x15785.gb_ov
capb_chick.sw         gap.pair
gcg2 18% pileup @capb.txt

PileUp creates a multiple sequence alignment from a group of related
sequences using progressive, pairwise alignments.  It can also plot a
tree showing the clustering relationships used to create the alignment.


   1      CAPB_CHICK   277 aa
   2      CAPB_MOUSE   277 aa
   3      CAPB_HUMAN   272 aa
   4      CAPB_CAEEL   270 aa

 What is the gap creation penalty (* 8 *) ?

 What is the gap extension penalty (* 2 *) ?

 This program can display the clustering relationships graphically.
 Do you want to:

     A) Plot to a FIGURE file called "pileup.figure"
     B) Plot graphics on HP7550 attached to /dev/tty15
     C) Suppress the plot

 Please choose one (* A *):

 The minimum density for a one-page plot is 4.0 sequences/100 platen units.
 What density do you want (* 4.0 *) ?

 What should I call the output file name (* capb.msf *) ? list.msf

 Determining pairwise similarity scores...

   1   x     2       5.14
   1   x     3       4.79
   1   x     4       3.63
   2   x     3       4.82
   2   x     4       3.62
   3   x     4       3.63

 Aligning...

   1     .............-..
   2     .............-.
         .............-..
   3     .............-.
         .............-..

 FIGURE instructions are now being written into pileup.figure.


        Total sequences:          4
       Alignment length:        278
               CPU time:      00.34

            Output file:/disk2/usr/people/petang/LECTURE5/list.msf