Phylogenetic Tree

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  • Topic: Computational phylogenetics, Phylogenetic tree, Phylogenetics
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LAB 6

Construct Phylogenetic Tree Using cyt b Gene
(Barry G Hall, Phylogenetic Tree made Easy , A How to Manual

Introduction

Evolutionary tree also known as phylogenetic tree is describing a system of clustering and classification of related organism that aims to show their evolutionary history. It is a diagram depicting the evolutionary relationships between species or groups of organisms as usually dichotomously branching lines to form a treelike pattern. In some trees, changes in the relative abundance of a lineage are indicated by the width of the branch.(Oxford, dictionary) In this experiment we will use MEGA software (Kumar et, al. 2004).

MEGA (Kumar et al. 2004) is a modern, integrated phylogenetics package that elegantly handles downloading sequences through its own specialized web browser, aligning sequences through its implementation of ClustalW, estimating phylogenetic trees by a variety of distance methods including Neighbor Joining (NJ), and drawing those trees in a variety of ways. MEGA is free and can be downloaded from http://www.megasoftware.net.

Procedure

1. You will compare the sequences of the partial cyt b genes from birds, fish mammals and ext. At the end of the exercise, you can compare your results with each other to determine whether your different nucleotides showed the same evolutionary relationships between species of all organisms. ⇨ NOTE: make sure you are working individually and do not choose the same species with your partner. 2. Use BLAST to search for sequences related to cyt b gene. In the MEGA main window, from the alignment window choose Do BLAST search. Copy the DNA sequence of Luciana from file and paste the sequence into the search box on the BLAST page. 3. Decide which related sequences to include on your tree.

4. Download the sequence and save this sequence to your computer in FASTA format. After you had saved all the sequence you wanted to include on...
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