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Phylogenetic Trees

Phylogenetic Trees. Importance of phylogenetic trees What is the phylogenetic analysis Example of cladistics Assumptions in cladistics Frequently used terms Fundamentals of Phylogenetc models Phylogenetic software. Importance of Phylogenetic Tree.

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Phylogenetic Trees

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  1. Phylogenetic Trees • Importance of phylogenetic trees • What is the phylogenetic analysis • Example of cladistics • Assumptions in cladistics • Frequently used terms • Fundamentals of Phylogenetc models • Phylogenetic software

  2. Importance of Phylogenetic Tree • Classification is important to understand • Evolutionary history of an Organism • Study of Biological Diversity • Organization • Progressive Multiple Sequence Alignment

  3. What is Phylogenetic Analysis • Study of evolutionary relationship • Inferring or estimating relationship • Usually presented as branching, tree • Gene Tree: Inherited relatioships • It is also called cladistics • clade means branch in Greek • Member of group/clade share a common rel.

  4. Example of Cladistics

  5. Assumptions in Cladistics • Any group of oragnisms is related by descent from a common ancestor • Members of a group or clade share common evolutionary history • A group sharing a unique feature, different from other groups • There is bifurrcating pattern of cladogenesis • Change in charterstics occurs in lineages over time

  6. Frequently Used Terms • Clade: A monophyletic taxon. Clades are group of organisms • Taxon: Named group or organisms but not necessarily a clade • Branch Length: In some case it repersent divergence • Node: A bifurcating branch point

  7. Fundamentals of Phylogenetic Models • Sequence alignment (AMPS,Clustal-W) • Substitution model (weight model) • Rates between Bases • Site Substitution(overall compositional change) • Tree building • Tree Evaluation

  8. Tree Building • Distance Based Methods • UPGMA: Unweighted Pair Group Method It is a Clustring algorithm, it cluster tree branches based on greatest similarity among pairs and averages of joined pairs • NJ: Neighbor Joining First, it join nearest pair in start and then continue till one remain • Character-Based • Maximum Parismony (MP) • Maximum Likelihood (ML)

  9. Tree Evaluation • Randomize Tree • Randomize Character Data • Bootstrap • Likelihood Test

  10. PHYLIP • PAUP • PUZZLE • TreeDraw • MACCLAD • Web Based • webphylip, PhyloBlast

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