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Phylogenetics

Tutorial: Constructing phylogenetic tree using MEGA7

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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].

Preparing input

Save protein sequences in FASTA format in a file, here named as ‘sequences.fasta’. We are using around 20 sequences of average length. If you are going to use a large number of protein sequences, then try to construct the tree on a workstation otherwise it will crash and you will not get any output. A phylogenetic tree is constructed in the following steps using MEGA7:

1. Aligning sequences

At first, align all input sequences as shown below.

  • Go to Align (dropdown) --> Edit/Build Alignment --> Retreive sequences from a file --> OK.
  • Select your input file, here sequences.fasta. A new window will open showing all the sequences.
  • Go to Edit --> Select Allor simply press Ctrl+A.
  • Go to Alignment --> Align by ClustalW --> Align Protein --> OK. At this step, you can parameters of alignment but we are aligning using default values. You can align sequences by MUSCLE by selecting Align by MUSCLE instead of selecting Align by ClustalW from the Alignment option at the top menu bar.
  • After processing, it will show you the aligned sequences in the same window.
  • If you want to save the session, then go to Data --> Save Session. Select the appropriate folder and click Save.

2. Exporting into the MEGA format

We need the aligned sequences in the MEGA format for constructing the phylogenetic tree. To convert into the MEGA format, follow the steps mentioned below:

  • Go to Data --> Export Alignment --> Mega Format. You can also export into other formats such as FASTA, Phylip/Paup at this step.
  • Select the appropriate folder and click Save.

3. Constructing the phylogenetic tree

You can construct different kinds of trees such as ML, Neighbor-Joining, Maximum Parsimony, and so on depending upon your data. We are constructing an ML tree in this tutorial.

  • Go to the main window of MEGA7. Click Phylogeny --> Construct/Test Maximum Likelihood Tree.
  • Select the converted file (.meg) and click Open. 
  • A new window will appear ‘Analysis Parameters’. Here you can set different values such as bootstrapping value, substitution model, and so on. It is recommended to test phylogeny by bootstrapping for 500-1000 times. Additionally, select the substitution model appropriately. You can use other software such as Prottest3 to find an appropriate model for your data. See this article.
  • After setting parameters, click Compute. It will take time depending upon the number of sequences and bootstrap values.
  • Finally, it will show you the constructed tree. You can save the tree session and export it into Newick format.

References

  1. Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology and evolution33(7), 1870-1874.

 

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

Phylogenetics

How to find a best fit model using IQ-TREE?

Dr. Muniba Faiza

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How to find a best fit model using IQ-TREE?

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…)

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Phylogenetics

Installing TREE-PUZZLE on Ubuntu

Dr. Muniba Faiza

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Installing tree-puzzle on Ubuntu

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…)

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Phylogenetics

Update: A multi-epitope in silico vaccine candidate designed for Covid-19

Dr. Muniba Faiza

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covid19-vaccine

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…)

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Phylogenetics

Phylogenetics analysis of SARS-CoV-2 spike glycoproteins

Dr. Muniba Faiza

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Phylogenetic Tree of Covid Corona Virus with other Species

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…)

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Phylogenetics

Installing and executing ProtTest3 on Ubuntu

Dr. Muniba Faiza

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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…)

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Phylogenetics

How to calculate dN, dS, and dN/dS ratio on a set of genes using MEGA?

Dr. Muniba Faiza

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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…)

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Phylogenetics

Most widely used tools for phylogenetic tree customization

Dr. Muniba Faiza

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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…)

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Phylogenetics

Why To Study Evolution?

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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. (more…)

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Phylogenetics

Molecular Evolutionary Genetic Analysis

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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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Phylogenetics

Monogenea: An Easy Portfolio for Molecular Phylogenetics

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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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