Phylogenetics often refers to the evolutionary study of the organisms in a pedigree forming a tree that is called as the phylogenetic tree. A phylogenetic tree is a visual representation of the relationship between different organisms, showing the path through evolutionary time from a common ancestor to different descendents. They're as good as the data on which they'rebased. The tree branching patterns representing the evolutionary divergence are referred to as phylogeny.
Similarities and divergence among related biological sequences revealed by sequence alignment often have to be rationalized and visualized in the context of phylogenetic trees. Thus, molecular phylogenetics is a fundamental aspect of bioinformatics. Molecular phylogenetics uses the structure and function of molecules and how they change over time to infer these evolutionary relationships.
Recovering true historical relationships between any groups of species, genes or proteins is one of the principal goals of evolutionary research. Knowledge of phylogeny tells us about the pattern of evolutionary relationships, revealing the historical pattern of speciation and divergence and enabling us to classify life according to evolutionary scheme. Moreover, it is important because of its wide applications throughout biology such as in studies of human diseases for epidemiological investigations, for identifying and characterizing newly discovered pathogens and for identifying and tracking natural reservoirs of zoonotic diseases.
Many phylogenetic trees are built using the morphology of organisms or fossils. The genes are the medium for recording the accumulated mutations; they can serve as molecular fossils. Through comparative analysis of the molecular fossils from a number of related organisms, the evolutionary history of the genes and even the organisms can be revealed. There are several bioinformatics tools and databases that can be used for phylogenetic analysis. These include PANTHER, PFam, TreeFam, iTOL, FigTree. iTOL stands for interactive Tree Of Life, which is an online phylogenetic tree viewer tool. It's used to make visual changes in the design of the phylogenetic tree. FigTree is a stand-alone program, designed as a graphical viewer of phylogenetic trees.
MEGA is the most commonly used tool in Bioinformatics for phylogenetic analysis. It uses different algorithms to build phylogenetic trees based on different methods, i.e, Maximum likelihood, Neighbour-Joining, Minimum-Evolution, UPGMA, and Maximum Parsimony tree generating methods.
To learn the detailed step by step method to carry out phylogenetic analysis of the sequences, you can find the tutorial videos in the Gray Bioinformatics sections at BioCode. The Phylogenetic Analysis videos cover the creation, visualization and use of the Phylogenetic tree which helps in the various research and practical fields.