Constructing Phylogenetic Tree using UPGMA Method
UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a distance-based method for constructing phylogenetic trees. It works by iteratively clustering the two closest groups of sequences together, forming a new cluster until all sequences are grouped into a single tree. The distances between clusters are calculated using the average of all pairwise distances between sequences within those clusters. UPGMA produces rooted trees, meaning it has a defined root representing the common ancestor. Here's a more detailed explanation: 1. Distance Matrix UPGMA begins with a distance matrix, which contains the pairwise distances between all sequences being compared. These distances can be based on sequence alignment, protein structure comparisons, or other relevant metrics. \[D_{i,j}=\max\begin{cases}D_{i-1,j-1} & + & s(a_i,b_j) \\D_{i-1,j} & + & s(a_i,-) \\D_{i,j-1} & + & s(-,b_j)\end{cases}=\max\begin{cases}D_{i-1,j-1}& + ...
