Clinical Microbiology: Open Access

A Note on Analysis of Molecular Phylogenetics

Amey Coban^* Department of Microbiology and Clinical Microbiology, Ondokuz Mayis University Medical School, Samsun, Turkey
^*Correspondence: Amey Coban, Department of Microbiology and Clinical Microbiology, Ondokuz Mayis University Medical School, Samsun, Turkey, Email:

Received: 06-Dec-2021 Published: 29-Dec-2021

About the Study

Molecular phylogenetics is a branch of phylogenetics that studies genetic and hereditary molecular variations, mostly in DNA sequences, to determine an organism's evolutionary relationships. It is feasible to deduce the processes that have resulted in species variety from these investigations. A phylogenetic tree is a representation of the results of a molecular phylogenetic investigation. Molecular phylogenetics is a subset of molecular systematics, which encompasses the application of molecular data to taxonomy and biogeography.

Molecular phylogenetics and evolutionary biology are linked. The process of selecting changes (mutations) at a molecular level throughout numerous branches of the tree of life is known as molecular evolution. Molecular phylogenetics is the process of inferring evolutionary links that emerge as a result of molecular evolution and constructing a phylogenetic tree.

Molecular phylogenetic analysis

A molecular phylogenetic analysis can be accomplished using a variety of methodologies. One method is available at Nature Protocol, which includes a comprehensive step-by-step protocol for constructing a phylogenetic tree, which includes DNA/ Amino Acid contiguous sequence assembly, multiple sequence alignment, model-test and Maximum Likelihood and Bayesian Inference are used to reconstruct phylogenies. The acquisition of sequences is the initial stage. The next stage involves completing a multiple sequence alignment, which is the foundation for building a phylogenetic tree. Different DNA and amino acid substitution models are included in the third stage. There are several substitution models. Hamming distance, the Jukes and Cantor one-parameter model, and the Kimura two-parameter model are a few examples (see Models of DNA evolution). The fourth step includes several tree-building approaches, such as distance-based and character-based methods. The degree of divergence and the likelihood that a nucleotide changes to another are calculated using the normalised Hamming distance and the Jukes-Cantor correction formulas, respectively.

Unweighted Pair Group Method Using Arithmetic Mean (UPGMA) and Neighbor joining, distance-based approaches, Maximum parsimony, a character-based method, and Maximum likelihood estimation and Bayesian inference, both characterbased/ model-based methods, are all common tree-building methods.

Although UPGMA is a straightforward procedure, it is less accurate than neighbor-joining. Last but not least, the trees must be evaluated. Consistency, efficiency, and robustness are all factors in this accuracy evaluation. Molecular Evolutionary Genetics Analysis (MEGA) is a user-friendly and free to download and use analytic software. Both distance-based and character-based tree techniques can be analysed with this software. MEGA also includes a number of options, like as heuristic techniques and bootstrapping that can be used. The broader category of resampling procedures includes any test or measure that incorporates random sampling with replacement, and bootstrapping is one of them. Bootstrapping assigns accuracy measures to sample estimates such as bias, variance, confidence intervals, and prediction error. This procedure can estimate the sampling distribution of nearly any statistic using random sampling methods.

When sampling from an approximate distribution, bootstrapping estimates the attributes of an estimator (such as its variance) by measuring those properties. The empirical distribution function of the observed data is a common choice for an approximation distribution. When a collection of observations can be considered to come from an independent and uniformly distributed population, this can be accomplished by producing a number of resamples of the observed data set with replacement. Bootstrapping is a method for determining the robustness of topology in a phylogenetic tree by calculating the proportion of replicates that each clade is supported by. In general, a percentage of more than 70% is considered noteworthy. The flow chart on the right shows the order in which the five stages of Pevsner's molecular phylogenetic analysis technique have been described.