Table 1.
A hierarchy of probabilistic alignment models
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aIndel rate parameter.
bMixture coefficient of mixture geometric indel-length distribution.
cParameters of geometric indel-length distribution.
dSignifies that average parameters are used (Supplemental Table S2).
eSignifies that parameters depend on the fraction GC (see Supplemental Table S2).
fSignifies that substitution rate parameters are tuned to the local sequence divergence (see Supplemental Table S3). All explicit parameter values are averages (see Supplemental Table S2).
