November 2017
Intermediate to advanced
472 pages
11h 21m
English
book
Basic Applied Bioinformatics
by Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal
Content preview from Basic Applied Bioinformatics
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CHAPTER 26Construction of Phylogenetic Tree Using MEGA7
CS Mukhopadhyay and RK Choudhary
School of Animal Biotechnology, GADVASU, Ludhiana
26.1 INTRODUCTION
The Molecular Evolution and Genetic Analysis (MEGA) is a freely downloadable (for research and education) integrated tool for analyzing molecular data (nucleotide and protein sequences) and construction of phylogenetic trees. The latest version, MEGA 7.0.14, is used for some bio‐computational analyses, for example in: sequence alignment; determining the best evolutionary model; construction of phylogenetic trees as well as inferring ancestral sequences; mining online databases; estimation of divergence times; rates of molecular evolution; and testing evolutionary hypotheses. The software is freely available at http://www.megasoftware.net/ and can be run in Windows (both GUI and command‐line‐based), as well as in Linux and Mac operating systems (command‐line‐based).
In this chapter, we will see how a phylogenetic tree can be constructed using MEGA7 suit and inferred.
26.2 OBJECTIVE
To build a phylogenetic tree from a given set of molecular sequences.
26.3 PROCEDURE
26.3.1 Prepare the sequence file
Download and then arrange the molecular sequence data (nucleotide or amino acid sequences) in FASTA format, and save in a notepad (*.txt) file. It is not necessary that all the sequences should be of the same length, but the sequences should be homologous (depending on the hypothesis being tested in the experiment). The descriptive ...
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