See also
Fastest options
Most accurate options
Compromise options for
large datasetsThe default MUSCLE
algorithm is summarized in the following table. The -maxiters option can be used
to choose how many of these iterations are performed, allowing a choice between
higher accuracy (more iterations) and higher speed (fewer iterations). By
default, MUSCLE will attempt up to 16 iterations but will terminate earlier if
no changes have been made after one full refinement iteration.
|
Iteration |
Steps |
Method |
|
1 |
1a. Distance matrix |
k-mer counting. Can be changed by
-distance1 option. |
|
1b. Tree building |
UPGMB. Can be changed by -cluster1
option. |
|
1c. Alignment |
Progressive alignment by tree.
|
|
2 |
1a. Distance matrix |
Kimura distance from MSA built in first
iteration. Can be changed by ‑distance2
option. |
|
1b. Tree building |
UPGMB. Can be changed by -cluster2
option. |
|
1c. Alignment |
Progressive alignment by new tree.
|
|
3, 4, 5... |
Refinement |
The guide tree is split at every branch. A
split divides the current multiple alignment into two profiles, which are
re-aligned using profile-profile alignment.
The new MSA is kept if the objective score is improved.
|
|