I've tried to search a bit first, but have been unable to find a quick answer. In the documentation for biopython I come across this:
#Distance is calculated based on the number of shared 6mers.
This is the default alignment algorithm for MAFFT. What is a 6mer?
Also when should I choose the alternatives over the 6mer pairwise alignment? Those alternatives are:
- Needleman-Wunsch (global pairwise)
- Smith-Waterman (local pairwise)
- Local pairwise with generalized affine gap cost (Altschul 1998)