

doublet_align:     
  Fast Protein Sequence Alignment using Doublet Scores 
  and the Crooks-Green dynamic programming algorithm.

  make              : Compile the  code
  doublet_align -h  : print usage infomation


directories
  stats     : Source code of res_stats, used by doublet_align
  data	    :  Default doublet matrix and example sequence data


Examples
 Align one sequence agaonst another using default parameters.
 ( -S 0 turns off statistics, -D displays the alignment)
  
   ./doublet_align -S 0 -D data/AST1.fa data/AST2.fa

 Search a sequence database for matches against a single sequence.
 
   ./doublet_align data/AST1.fa data/astral1.35.40.seg.fa

