BioGem Blog

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}& + ...

BioEdit is a free biological sequence alignment editor. It has an intuitive multiple document interface and offers convenient features that make alignment and manipulation of sequences relatively easy on windows desktop computers. Additionally, there are several sequence manipulation and analysis options and links to external analysis programs that facilitate a working environment, allowing users to view and manipulate sequences with simple point-and-click operations. The BioEdit software provides automated local and web BLAST ( B asic L ocal A lignment S earch T ool) searches with a simple graphical user interface (GUI) to the command-line BLAST program. This is a simple video tutorial on how to construct a custom nucleotide/protein database using BioEdit software to support NCBI BLAST . The tutorial also covers how to perform a query search, specifically pairwise sequence alignment, against the database.