Read a multiple alignment in PIR 
 or FASTA format and output a matrix of
 Euclidean distances for SPACER.


  The sequences must be aligned already!
  Use PIR or FASTA format with hyphens for gaps.

 Multiple alignment file ?        >> 
 Name for output (matrix) file ?   [  alignment.dist ] >> 
 Name for output (matrix) file ?   [  alignment.dist ] >> 
 Number of sequences =           12

 Consensus length    =          156


 Sequence #    1HBA$ELEMA        length =   141
 Sequence #    2HBA$PHOVI        length =   141
 Sequence #    3HBA$PHYCA        length =   141
 Sequence #    4HBA$PONPY        length =   141
 Sequence #    5HBBA$CAPHI       length =   145
 Sequence #    6HBBL$XENLA       length =   146
 Sequence #    7HBBZ$MOUSE       length =   147
 Sequence #    8HBD$AOTTR        length =   146
 Sequence #    9MYG$CALJA        length =   153
 Sequence #   10MYG$CANFA        length =   153
 Sequence #   11MYG$CASFI        length =   153
 Sequence #   12MYG$CEBAP        length =   153

  Type 1 to toss all gaps; 0 not to [1] >>   Type 1 for DNA; 0 for protein     [0] >> 
  Type 1 for ID distances; 0 for Smith aa matrix [1] >>   Type 1 for ID distances; 0 for Smith aa matrix [1] >>   Type 1 for ID distances; 0 for Smith aa matrix [1] >>