Subjects of this lecture

18/3/04


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Table of Contents

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Subjects of this lecture

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Phylogenetics - WHY?

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From a common ancestor sequence, two

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One of the most striking features of life is all living organisms share �highly conserved regions� in proteins, particularly in proteins that are involved in information processing (transcription and translation).

Relationships of Phylogenetic Analysis and Sequences Analysis

How we calculate the Degree of Divergence

Relationships of Phylogenetic Analysis and Sequences Analysis

Relationships of Phylogenetic Analysis and Sequences Analysis

Relationships of Phylogenetic Analysis and Sequences Analysis

What is a phylogenetic tree?

What is a phylogenetic tree?

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In a phylogenetic tree...

In a phylogenetic tree...

Tree structure

Slide taken from Dr. Itai Yanai

The Molecular Clock Hypothesis

Rooted Tree = Cladogram

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Rooted versus Unrooted

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Selecting sequences for phylogenetic analysis

Selecting sequences for phylogenetic analysis

Known Problems of Multiple Alignments

Known Problems of Multiple Alignments

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Known Problems of Multiple Alignments

Selecting sequences for phylogenetic analysis

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Taken from Dr.Itai Yanai

Building Phylogenetic Trees

Character Based Methods

Character Based Methods

Character Based Methods

Character Based Methods - Maximum Parsimony

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Character Based Methods - Maximum Parsimony

Character Based Methods - Maximum Parsimony

Maximum Parsimony Methods are Available�

Character Based Methods - Maximum Likelihood

Character Based Methods - Maximum Likelihood

Maximum Likelihood method

Distances Methods

Distances Matrix Methods

Distances Matrix Methods

Common steps to build a TREE used by Distances method

Distance method steps

Distances Matrix Methods

Statistical Methods

Statistical Methods

Taken from Dr. Itai Yanai

Taken from Dr. Itai Yanai

Statistical Methods

Mutations in DNA as a source for evolutionary analysis

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DNA Substitution Mutations

Correction for likelihood of mutations in DNA sequences

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These evolutionary models improve the distance calculations between the sequences.

DNA Evolution Models

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How to draw Trees? (Building trees software)

A Tip...

Known problems of Phylogenetic Analysis

Known problems of Phylogenetic Analysis

Known problems of Phylogenetic Analysis

How many trees to build?

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Author: weizmann

Email: irit.orr@weizmann.ac.il