sim.c is the C source code of a local similarity program,
a space-efficient implementation of the Smith-Waterman algorithm.

cap.c is the C source code of a fragment assembly program.

lcp.c is the C source code of a program for identifying regions of
a sequence satisfying local content requirements.

gap.c is the C source code of a program for computing an optimal
alignmnet of two sequences, where terminal gaps are not penalized
and long internal gaps in the shorter sequence are given a constant penalty.

map.c is the C source code of a program for computing a multiple alignment
of sequences, where terminal gaps are not penalized and long internal gaps
in shorter sequences are given a constant penalty.

gta.c is the C source code of a program for computing
an optimal global alignment of three sequences
using dynamic programming and divide-conquer techniques.
The program takes cubic time and quadratic space.

cda.c is the C source code of a program for computing
an optimal global alignment of two sequences,
where a context-dependent scoring scheme is used.

PAM250 is a scoring matrix used by SIM, GAP, MAP, GTA, NAP, LAP,
and DPS for comparisons involving protein sequences.

BLOSUM62 is a scoring matrix used by SIM, GAP, MAP, GTA, NAP, LAP,
and DSP for comparisons involving protein sequences.

CAP2 is the directory containing the executable of
the CAP2 program under SunOS, Solaris, Irix, and Dec OSF/1, respectively.

nap.c is the C source code of a program for computing
a global alignment of a DNA sequence and a protein sequence.

lap.c is the C source code of a program for computing
a local alignment between a DNA sequence and a protein sequence.

dps.c is the C source code of a program for comparing a DNA sequence
with a protein database.

AAT is a directory containing the executable of the AAT package
under Sun Solaris.

GSA2 is a directory that contains sequence statistics
for a gene structure assembly program named GSA2.