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Steps to construct a phylogenetic tree using MEGA software

The document outlines the steps to construct a phylogenetic tree using MEGA software, starting from obtaining and formatting sequence data to viewing and saving the tree. It details the process of aligning sequences, selecting tree-building methods, and interpreting the resulting tree with emphasis on bootstrap values indicating the strength of evolutionary relationships among various organisms. The tree illustrates relationships between RNA polymerase sequences of different organisms, highlighting strongly, moderately, and weakly supported groupings based on bootstrap values.

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5 views3 pages

Steps to construct a phylogenetic tree using MEGA software

The document outlines the steps to construct a phylogenetic tree using MEGA software, starting from obtaining and formatting sequence data to viewing and saving the tree. It details the process of aligning sequences, selecting tree-building methods, and interpreting the resulting tree with emphasis on bootstrap values indicating the strength of evolutionary relationships among various organisms. The tree illustrates relationships between RNA polymerase sequences of different organisms, highlighting strongly, moderately, and weakly supported groupings based on bootstrap values.

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Mentee
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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 Steps to construct a phylogenetic tree using MEGA software

1. Obtain and Format Sequence Data:

 Gather the DNA or protein sequences you want to analyze.


 Ensure your sequences are in a compatible format. MEGA primarily uses its
own .meg format, but it can also import other common formats like FASTA,
GenBank, and Phylip.

2. Open Sequence Data in MEGA:

 Click on File in the main menu.


 Select Open and browse to your sequence file.

3. Align the Sequences (if not already aligned):

 If your sequences are not yet aligned, Choose an alignment algorithm.


ClustalW and MUSCLE are common choices available in MEGA. Select
the one you prefer.
 Once you are satisfied with the alignment, go to File in the Alignment
Explorer and select Save Alignment. Choose the MEGA format (.meg) to
ensure compatibility for tree building.

4. Build the Phylogenetic Tree:

 Close the Alignment Explorer and return to the main MEGA window.
 Click on the Phylogeny tab in the main menu.
 Select one of the tree-building methods available. Common methods
include:
o Construct/Test Neighbor-Joining (NJ) Tree: A distance-based
method that is relatively fast.
 A dialog box will appear asking for the data file. Select the .meg file you
saved in the previous step.
 Another dialog box with analysis parameters will open.
 Click Compute or OK to start building the tree.

5. View and Analyze the Phylogenetic Tree:

 Once the tree construction is complete, the Tree Explorer window will open,
displaying the phylogenetic tree.

6. Save or Export the Phylogenetic Tree:


 To save the tree for later use or publication, go to File in the Tree Explorer
menu.
 You can save the tree in various formats, including:

o Save Current Tree as Newick File (.nwk)


o Save as MEGA Tree File (.mtf)
o Export as Graphics: Export the tree as an image file (e.g., PDF,
PNG, TIFF) for use in reports or publications.

 PHYLOGENETIC TREE SHOWING RELATIONSHIP BETWEEN SEQUENCE OF


RNA POLYMERASE OF DIFFERENT ORGANISMS

Here's a breakdown of what the tree shows:


 Taxa: The labels at the ends of the branches (HUMAN, FRUIT FLY, RAT,
LIZARD, FUNGI, FROG, BACTERIA, PLANT, FISH, BAT) represent the
different organisms being compared.
 Branches: The lines connecting the taxa represent the evolutionary
relationships between them. The length of the horizontal branches can
sometimes be proportional to the amount of evolutionary change, but in this
case, the scale bar indicates a general measure of distance.
 Nodes: The points where branches meet represent hypothetical common
ancestors.
 Bootstrap Values: The numbers (e.g., 100, 77, 52, 41, 87, 99) at the nodes
indicate the support for the grouping of the taxa that originate from that
node.

Interpretation of the Tree:

 Strongly Supported Relationships (High Bootstrap Values):


o The grouping of HUMAN, FRUIT FLY, RAT, and LIZARD is very
strongly supported (100). This suggests a close evolutionary
relationship among these animals.
o Within this group, HUMAN and FRUIT FLY are strongly supported
as being more closely related to each other than either is to RAT or
LIZARD (100).
o FISH and BAT are also strongly supported as being closely related
(99).
 Moderately Supported Relationships:
o The grouping of FUNGI and FROG has moderate support (77),
suggesting a reasonably supported evolutionary link.
o The broader grouping that includes (HUMAN, FRUIT FLY, RAT,
LIZARD) and (FUNGI, FROG) has moderate support (52).
o The grouping of BACTERIA and PLANT has moderate support (87).
 Weakly Supported Relationships (Low Bootstrap Values):
o The deepest node, which connects the (HUMAN, FRUIT FLY, RAT,
LIZARD, FUNGI, FROG) group with the (BACTERIA, PLANT,
FISH, BAT) group, has weak support (41). This indicates that the
evolutionary relationships at this deeper level are less certain based on
the data used to construct this tree.

In summary, this bootstrap consensus tree visually represents the


inferred evolutionary relationships between the listed organisms, with
the bootstrap values providing a measure of confidence in those
relationships. Higher bootstrap values indicate more robust and reliable
groupings.

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