SIM is a directory containing the following:
       sim.c: the C source code of a local similarity program,
       PAM250: the scoring matrix used by SIM for protein comparisons,
       seq1 and seq2: two sample DNA sequences.

CAP is a directory containing the following:
       cap.c: the C source code of a fragment assembly program,
       gels: a sample file of fragments.

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 and LAP
for comparisons involving protein sequences.

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

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.
