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Phylogenetic Tree Construction Guide

UPGMA constructs a tree using sequential clustering that assumes constant evolutionary rates. Neighbor joining builds trees using residual distance matrices without assuming equal rates. Maximum parsimony selects the tree that requires the fewest evolutionary changes. Maximum likelihood chooses the tree with the highest probability of reflecting the actual evolutionary process, examining all possible trees and site patterns.

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281 views4 pages

Phylogenetic Tree Construction Guide

UPGMA constructs a tree using sequential clustering that assumes constant evolutionary rates. Neighbor joining builds trees using residual distance matrices without assuming equal rates. Maximum parsimony selects the tree that requires the fewest evolutionary changes. Maximum likelihood chooses the tree with the highest probability of reflecting the actual evolutionary process, examining all possible trees and site patterns.

Uploaded by

Nj Nipom Jyoti
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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CONSTRUCTION OF PHYOGENETIC TREE USING UPGMA,

NEIGHBOUR JOINING, MAXIMUM PARSIMONY & MAXIMUM


LIKELIHOOD.
AIM:
To construct phylogenetic tree in order to find the relatedness among the
organism using distance based tree construction method.
DESCRIPTION:
UPGMA construct a tree using simple sequential clustering methods and its
simplest of all clustering methods. It takes unwanted distance and is based on
assumption that taxa evolve at a constant rate and they are equidistant from
the root. They employ sequential clustering algorithm in which local
topological relationships are identified in the order of similarity and
phylogenetic tree is built in a step were manner owing to its fast speed of
calculation it has found extensive usage in clustering analysis of DNA
microarray data.
Neighbour joining is another distance based method which is similar to
UPGMA. In this method it built the phylogenetic tree by using steps were
residual distance matrices it done not assume the taxa to be equidistant from
the root and connect with unequal evolutionary rates between sequences a
conversion step.
Maximum parsimony is a character based method which states that the
simplest explanation is probably correct one. The principle of this method says
that least number of mutations is probably the best way to explain difference
among the taxa underity.
Maximum likelihood uses probabilistic model to choose a best tree that
gives highest probability /likelihood. It finds a tree that most likely reflect the
actual evolutionary process . maximum likelihood is an exhaustive method that
searches every possible tree topology and considerative every position in an
alignmeng of both informative and non informative sites.
QUERY:
NAME OF THE GENE – CD24:
PROCEDURE:
1. Open MEGA software.
2. Go to align button and select edit / build alignment icon.
3. Create a new alignment by selecting the type of data we want to do .
4. Insert the sequence from the file (save the files in FASTA format).
5. Save the alignment in MEGA FORMAT .
6. Go to phylogeny and construct the required phylogenetic tree .
7. Select the MSA file in MEGA format and click ok with default
parameters.
8. The respective phylogenetic tree would be constructed and displayed.
9. Write interpretation for result.

MEGA HOMEPAGE

MAXIMUM LIKELIHOOD :

NEIGHBOR JOINING:
MINIMUM EVOLUTION:

UPGMA:
MAXIMUM PARSIMONY:

RESULTS AND DISCUSSIONS:


THE phylogenetic trees were successfully constructed using UPGMA, NT, MAXIMUM PARSIMONY,
MINIMUM EVOLUTION , MAXIMUM LIKELIHOOD.

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