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How to Make A Phylogenetic Tree From DNA Sequences

Madison Pascual Munar has a Doctorate degree in Molecular Biotechnology.


The Blueprint of Life: Deoxyribonucleic Acid or DNA

Deoxyribonucleic Acid or DNA is a universal attribute of every living organism. The advent of DNA sequencing has allowed the elucidation of evolutionary relationships among organisms. It has unlocked the mystery behind the human ancestry. DNA is made up of four nucleotide bases, namely adenine (A), thymine (T), guanine (G), and cytosine (C). The combination of the three nucleotide bases is called codons or the triplet code. A codon codes for an amino acid which later forms the proteins.

Genomic DNA or gDNA of an organism is now possible to be extracted. Once the gDNA is available, a plethora of analyses can be done. DNA sequencing has also improved ever since it was developed. Now, there are various industries which offers fast and accurate DNA sequencing platforms.

Open source Bioinformatics tools such as Basic Local Alignment Search Tool or BLAST is used to infer sequence homology using the DNA sequences. BLAST search will match the nucleotide bases from reported organisms in the National Center for Biotechnology Information or NCBI Database. Phylogenetic analysis using the DNA sequences and the information gathered from the BLAST search will determine the identity of the organism under study.

Analysis of the whole genome or the genetic make-up of an organism, including viruses, bacteria, protozoans, algae, fungi, insects, plants, and animals has far more implications aside from knowing one's identity. DNA sequences can also provide clues about the predisposition to a certain health conditions, and even explain how a certain population shows innate resistance to certain diseases.


Phylogenetic Analysis using Molecular Evolutionary Genetics Analysis (MEGA X)

Phylogenetic analysis is commonly employed to determine the evolutionary relationship of organisms. To perform a phylogenetic analysis, one has to know how to use a software called Molecular Evolutionary Genetics Analysis or MEGA Software which can be downloaded for free in the internet.

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Six Basic Steps to Construct A Phylogenetic Tree

This tutorial includes six basic steps in making a phylogenetic analysis using the MEGA X software. Just follow each step of the video tutorial, and you too can build your own phylogenetic tree.


Step-by-Step Video Tutorial

This is the step-by-step video tutorial on how to make a phylogenetic tree using the MEGA X software.

Phylogenetic Tree Construction Using MEGA X Software

Bioinformatics Tools

  • BLAST: Basic Local Alignment Search Tool
    The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
  • MEGA X
    MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

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