MUSCLE manual
Clustering (tree-building) options
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.