

aligneval.c   Comparison of pairwise and multiple sequence alignments
alignio.c     wrappers for i/o of sequence alignments
dayhoff.c     input of PAM tables, from BLAST's format
iupac.c       global definition of degenerate symbol info
msf.c         i/o of GCG MSF multiple sequence alignment format
refcoords.c   generation of reference coordinates for multiple sequence alignments
revcomp.c     reverse complement a nucleic acid sequence
rk.c          fast pattern searching for nucleic acids
selex.c       i/o of SELEX multiple sequence alignment format
seqencode.c   binary encoding of nucleic acid sequence
sqerror.c     squid_errno definition; Die(), Warn() error handlers
sqio.c        Don Gilbert's sequence format parsing; input of single sequences
sre_ctype.c   portability and extensions to ctype stuff
sre_math.c    various mathematical/seminumerical things
sre_string.c  portability and extensions to string.h stuff
types.c       type checking


