Editing Molecular phylogenetics (section)

==Molecular phylogenetic analysis==
There are several methods available for performing a molecular phylogenetic analysis. One method, including a comprehensive step-by-step protocol on constructing a phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly, [[multiple sequence alignment]], model-test (testing best-fitting substitution models), and phylogeny reconstruction using Maximum Likelihood and Bayesian Inference, is available at Nature Protocol.<ref name="Bast">{{cite journal |last1=Bast |first1=F. |title=Sequence Similarity Search, Multiple Sequence Alignment, Model Selection, Distance Matrix and Phylogeny Reconstruction |journal=Protoc. Exch. |date=2013 |doi=10.1038/protex.2013.065|doi-access=free }}</ref>

Another molecular phylogenetic analysis technique has been described by Pevsner and shall be summarized in the sentences to follow (Pevsner, 2015). A phylogenetic analysis typically consists of five major steps. The first stage comprises sequence acquisition. The following step consists of performing a multiple sequence alignment, which is the fundamental basis of constructing a phylogenetic tree. The third stage includes different models of DNA and amino acid substitution. Several models of substitution exist. A few examples include [[Hamming distance]], the Jukes and Cantor one-parameter model, and the Kimura two-parameter model (see [[Models of DNA evolution]]). The fourth stage consists of various methods of tree building, including distance-based and character-based methods. The normalized Hamming distance and the Jukes-Cantor correction formulas provide the degree of divergence and the probability that a nucleotide changes to another, respectively. Common tree-building methods include unweighted pair group method using arithmetic mean ([[UPGMA]]) and [[Neighbor joining]], which are distance-based methods, [[Maximum parsimony (phylogenetics)|Maximum parsimony]], which is a character-based method, and [[Maximum likelihood estimation]] and [[Bayesian inference in phylogeny|Bayesian inference]], which are character-based/model-based methods. UPGMA is a simple method; however, it is less accurate than the neighbor-joining approach. Finally, the last step comprises evaluating the trees. This assessment of accuracy is composed of consistency, efficiency, and robustness.<ref name="Pevsner">{{cite book |last=Pevsner |first=J. |date=2015 |title=Bioinformatics and Functional Genomics |publisher=Wiley-Blackwell |edition=3rd |chapter=Chapter 7: Molecular Phylogeny and Evolution |pages=245–295 |isbn=978-1-118-58178-0}}</ref>

[[File:Five Stages of Molecular Phylogenetic Analysis.png|800x80px|center|thumb|Five Stages of Molecular Phylogenetic Analysis]]

[[MEGA, Molecular Evolutionary Genetics Analysis|MEGA (molecular evolutionary genetics analysis)]] is an analysis software that is user-friendly and free to download and use. This software is capable of analyzing both distance-based and character-based tree methodologies. MEGA also contains several options one may choose to utilize, such as heuristic approaches and bootstrapping. [[Bootstrapping (statistics)|Bootstrapping]] is an approach that is commonly used to measure the robustness of topology in a phylogenetic tree, which demonstrates the percentage each clade is supported after numerous replicates. In general, a value greater than 70% is considered significant. The flow chart displayed on the right visually demonstrates the order of the five stages of Pevsner's molecular phylogenetic analysis technique that have been described.<ref name="Pevsner" />