## How does UPGMA method work?

UPGMA (unweighted pair group method with arithmetic mean) is a simple agglomerative (bottom-up) hierarchical clustering method. Thus the simple averaging in WPGMA produces a weighted result and the proportional averaging in UPGMA produces an unweighted result (see the working example).

## What is the time complexity of the UPGMA algorithm?

Complexity: The time and space complexity of UPGMA is O(n2), since there are n-1 iterations, with O(n) work in each one. ). If the solution to the least squares problem is 0, and there is a molecular clock (i.e., the solution is a clocklike tree), then UPGMA is guaranteed to return the optimal solution.

Is UPGMA an Ultrametric?

UPGMA is “ultrametric”, meaning that all the terminal nodes (i.e. the sequences/taxa) are equally distance from the root. In molecular terms, this means that UPGMA assumes a molecular clock, i.e. all lineages are evolving at a constant rate.

### What is the difference between UPGMA and neighbor-joining?

The key difference between UPGMA and neighbor joining tree is the type of the phylogenetic tree resulting from each method. UPGMA is the technique of constructing a rooted phylogenetic tree while neighbor joining tree is the technique of constructing an unrooted phylogenetic tree.

### Why is UPGMA an unreliable method in tree construction?

UPGMA is the simplest method for constructing trees. The great disadvantage of UPGMA is that it assumes the same evolutionary speed on all lineages, i.e. the rate of mutations is constant over time and for all lineages in the tree. Therefore, UPGMA frequently generates wrong tree toplogies!

What is the difference between UPGMA and Wpgma?

WPGMA is the same as UPGMA, except when shrinking the distance matrices, the new row and column values are no longer weighted by the number of taxa. Yes that’s right, Unweighted PGMA is based on weighted averages, and Weighted PGMA is based on unweighted averages. Good luck remembering this confusing difference!

## Why is UPGMA unreliable?

UPGMA is the simplest method for constructing trees. The great disadvantage of UPGMA is that it assumes the same evolutionary speed on all lineages, i.e. the rate of mutations is constant over time and for all lineages in the tree. This is called a ‘molecular clock hypothesis’.