Phylogenetics
Why To Study Evolution?
Understanding evolution is critical for understanding biology. As the preeminent scientist Theodosius Dobzhansky stated, “Nothing in biology makes sense except in the light of evolution.” Evolution is the only scientific explanation for the diversity of life. It explains the striking similarities among vastly different forms of life, the changes that occur within populations, and the development of new life forms. Excluding evolution from the science curricula or compromising its treatment deprives students of this fundamental and unifying scientific concept to explain the natural world.
The principles of evolution underlie improvements in crops, livestock, and farming methods. Natural selection accounts for the rise in pesticide resistance among agricultural pests and informs the design of new technologies to protect crops from insects and disease. Scientists are applying lessons from evolutionary biology to environmental conservation: plants and bacteria adapted to polluted environments are being used to replenish lost vegetation and to clean up toxic environments. Species from microbes to mammals adapt to climate change; studying the mechanism and rate of these changes can help conservation experts formulate appropriate measures to protect species facing extinction.
Understanding evolution is also central to the advancement of medicine. Indeed, the entire field of “evolutionary medicine” is devoted to using the principles of evolution to study and treat human illness and disease. Concepts such as adaptation and mutation inform therapies and strategies to combat pathogens, including influenza. Models developed by evolutionary biologists have shed light on genetic variation that may account for an increased risk of Alzheimer’s and coronary heart disease. Knowing the evolutionary relationships among species allows scientists to choose appropriate organisms for the study of diseases, such as HIV. Scientists are even using the principles of natural selection to identify new drugs for detecting and treating diseases such as cancer.
Studying evolution is an excellent way for students to learn about the process of scientific inquiry. Evolution offers countless and diverse examples of the ways scientists gather and analyze information, test competing hypotheses, and ultimately come to a consensus about explanations for natural phenomena. Understanding science is essential for making informed decisions and has become increasingly important for innovation and competitiveness in the 21st-century workplace. It is critical, therefore, that students receive a sound science education including evolution.
Removing evolution from the science classroom or allowing it to be compromised not only deprives students of a fundamental tenet of biology and medicine, but it will undermine their understanding of how scientific knowledge is amassed.
Previously, we have provided an installation tutorial for IQ-TREE on Ubuntu. In this article, we are going to perform model selection for a dataset using the standalone tool of IQ-TREE. (more…)
TREE-PUZZLE is a software to reconstruct phylogenetic trees using the maximum likelihood method [1,2]. It requires sequence data as input and implements a fast search algorithm and quartet puzzling. It can process large datasets easily. In this article, we will install TREE-PUZZLE on Ubuntu. (more…)
MEGAX is a bioinformatics software/tool used for phylogenetic tree construction. In this article, we will construct a maximum likelihood (ML) tree for a number of protein sequences using MEGA7 [1]. (more…)
Covid19 has created a great threat to human health. As you are aware, in this coronavirus outbreak, Bioinformatics Review has created a group, BiR-nCov19 Drug Development Team, to work on finding prevention to this disease. This research group consists of researchers from all over the world. (more…)
A novel coronavirus (CoV), named Severe Acute Respiratory Syndrome-CoV-2 (SARS-CoV-2) or nCoV-2019, has emerged since December 2019 from Wuhan city of Hubei province in China [1]. This virus belongs to the coronavirus family from which previous outbreaks have emerged (SARS and MERS). They have been a great threat to public health causing many deaths including SARS-CoV-2. There is no proper treatment available to cure this coronavirus disease (covid19). Scientists and researchers are trying really hard to develop a drug or a vaccine or a proper way to cure covid19. (more…)
Prottest3 is a software which is used to select a best-fit amino acid replacement model for a set of protein sequences [1]. ProtTest3 finds a best-fit model on the basis of the smallest value of one of three criteria: Akaike Information Criterion (AIC), Corrected Akaike Information Criterion, Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT) selected by the user. In this article, we will learn how to download and install the command-line version of ProtTest3 on Ubuntu. (more…)
If you want to get a quick idea about the non-synonymous vs synonymous (dN/dS) substitutions, you can easily use MEGA software [1]. Although HYPHY/Datamonkey provides the best results regarding selection pressure analyses. MEGA also uses HYPHY program [2] to calculate the dN/dS substitutions rate. Here is how you can do it. (more…)
Most of the times, it is a very tedious job to convert file formats in bioinformatics, especially when we are dealing with phylogeny. Most of the available online servers mess your file and the output format is also not supported by the other programs. Additionally, it is quite difficult to perform other customizations on the phylogeny tree. (more…)
MEGA: Molecular Evolutionary Genetic Analysis
It is important to know the basic molecular relationship between two living organisms as one begins performing comparative studies for knowing the evolutionary aspects and for contributing to knowledge base. Several tools and soft ware have been introduced for meeting the task of such analysis. Each tool has different algorithm and method to perform molecular phylogeny. Examples include; ClustalW, Dendroscope, Hyphy, PAUP and Phylip etc. Among them is the most efficient tool, MEGA, Molecular evolutionary phylogenetic analysis which performs both sequence analysis and phylogenetic analysis in a very sophisticated manner.
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Estimation of present day diversity of organism and understanding their diversity forms new cornerstones of conservation biology, evolutionary biology and ecology. Maintaining the totality of all texa from past to present and classifying into groups reflect how they have changed over the period of times. Necessarily, phylogenetics and evolutionary study of a particular group help out in knowing pattern of occurrence and relationships between two distantly related class or families and their descendents. (more…)
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