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# 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. 2010, BMC Bioinformatics). The next line tells LAST to use
# these gap costs:
#last -a 16 -b 1
# Let's also use a minimum alignment score of 90:
#last -e 90
# lastex suggests that 90 is not unreasonable for comparing mammalian
# genomes. In any case, you can override these parameters by setting
# options when running LAST. 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
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