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(N 2 ) 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.
|
|
