Options with names ending in 1 apply only to the first iteration. Option names
ending in 2 apply to iterations 2, 3 and later. Otherwise, the option applies to
all iterations. Default option value is shown in bold.
Option
Values
‑distance1
-distance2
-distance
kmer6_6:
Count 6mers in a compressed amino alphabet with 6 letters.
kmer20_3: Count 3mers in the full 20-letter amino acid
alphabet.
kmer20_4: Count 4mers in the full 20-letter amino acid
alphabet.
kbit30_3: Count 3mers in the full 20-letter amino acid
alphabet, using bit count to save space and increase speed (may be less
accurate).
-distance2
-distance
pctid_kimura: Kimura distance calculated from pair-wise percent identity.