# This matrix assigns a score of 2 to matches, -1 to transitions, and
# -2 to transversions.  When used with a gap existence cost of 16 and
# a gap extension cost of 1, it gives very sensitive and accurate
# alignments of distantly-related protein-coding sequences (MC Frith
# et al., manuscript in preparation).  The next line tells lastal to
# use these gap costs:
#lastal -a 16 -b 1
# Let's also use a minimum alignment score of 90:
#lastal -e 90
# The accompanying E-value tables suggest that 90 is not unreasonable
# for comparing gigabase-scale sequences.  In any case, you can
# override these parameters by setting options when running lastal.
# Finally, here is the matrix:

   A  C  G  T
A  2 -2 -1 -2
C -2  2 -2 -1
G -1 -2  2 -2
T -2 -1 -2  2
