MUSCLE manual
Distance options
 
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.

pctid_log: Log of Kimura distance.