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Constructing Phylogenetic Tree using UPGMA Method

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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}& + ...

Interactive Phylogenetic Tree Visualization using iTOL

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A phylogenetic tree ( a.k.a. , cladogram or dendrogram) is a diagrammatic/graphical representation of the genetical/evolutionary relationship of species/organisms/genes. Phylogenetic tree helps to find the common ancestor. The i nteractive T ree O f L ife ( iTOL ) is an online tool to display and manipulate phylogenetic trees. iTOL offers free access (limited access), standard subscription (unlimited access), and iTOL annotation editor subscription (unlimited and versatile access). It supports user-interactive customizable tree layouts, manual drawing, and annotation. iTOL can visualize trees with 50,000 or more nodes. This is a simple video tutorial for user interactive visualization of phylogenetic trees using the iTOL tool. The iTOL tool produces phylogenetic trees in various formats, such as rectangular, slanting, curved, radial, and curved. It accepts input in Newick, Nexus, or PhyloXML file format.

Constructing Phylogenetic Tree using MEGA Software

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A phylogenetic tree ( a.k.a. , cladogram or dendrogram) is a diagrammatic/graphical representation of the genetical/evolutionary relationship of species/organisms/genes. It helps to find the common ancestor. Construction of a phylogenetic tree consists of two phases, multiple sequence alignment and computing distance matrix. This is a simple video tutorial for constructing a phylogenetic tree using Molecular Evolutionary Genetics Analysis ( MEGA ) software. The MEGA software produces phylogenetic trees from multiple sequences in various formats: rectangular, slanting, curved, radial, and curved.