See also
Tree output files
The -cluster1 option applies to the first iteration,
-cluster2 applies to the second iteration, -cluster applies to iterations 1 and
2. Values for these options are shown in the table below.
| Value |
|
Description |
|
upgma |
|
Fast O(N2)
approximation to the textbook UPGMA algorithm.
|
|
upgmb |
|
Variant of
UPGMA (see papers). This is used by default for both iteration 1 and 2.
|
|
neighborjoining |
|
The
Neighbor-Joining algorithm. Better at making phylogenetic trees, but typically
worse for making guide trees for progressive alignment.Also slower. Usually not
recommended.
|
|