Changelog

Changes to suboptaln

0.06 
 yn00_cds_prealigned.c 
  a new program which will process multiple alignments and calculate all
  pairwise combination as the PAML yn00 does, will also accept multiple
  sequence files to process on the cmd line.

 squid/phylip.c
  modified to support really parsing multiple MSA alignments in a single file

 yn00_cds_optimal.c
  Will calculate alignments and dN, dS for all pairwise combinations not 
  just the first two sequences in the file.

  Also remove last codon of a sequence if it is a stop codon.

 
0.05 
 zuker.c  
  boundary condition error fixed in fill_matrix - should be offsetting
  location of best_loc by doing i-1

 yn00_cds_optimal.c 
  fixed bug which was caused by extra increment in cds_seq 

0.04 
 yn00_simple.c  
  Allow skipping of codons which contain a non-DNA char 
  (ambiguity bases or an N) so that can still calculate a distance value
  while skipping the codons which contain the character
   
  err2 now prints to stderr so that redirection capture is not cluttered
   with error/debugging messages.

0.03
 * Support --noheader options in yn00_cds_optimal and yn00_zuker_align