Phylogenetic Tree Computation Tutorial

15/6/02 Frank Olken - PGA PhylogenyTutorial1 Phylogenetic TreeComputation TutorialFrank OlkenLawrence Berkeley National LabPresentation to PGA CourseMay 3, 2002 Berkeley, California5/6/02 Frank Olken - PGA PhylogenyTutorial2 Overview Introduction: What? Why? .. Multiple Sequence Alignment Computing Phylogenetic Trees Merging Trees Resources Funding Sources25/6/02 Frank Olken - PGA PhylogenyTutorial3 Introduction5/6/02 Frank Olken - PGA PhylogenyTutorial4 Example Seq. A = A A C C G G T T Seq. B = A A C C G G T G Seq. C = A C C C G G T C Seq. D = A C C C G G T AABCDABCDU nrootedTreeRootedTree35/6/02 Frank Olken - PGA PhylogenyTutorial5 Similarity vs. Homology Similar sequences resemble one another Homolog sequences derived from common ancestor Ortholog homologous sequences within a species Paralog homologous sequences between species5/6/02 Frank Olken - PGA PhylogenyTutorial6 Ortholog vs. Paralog Ortholog genomic variation occurs afterspeciation hence can be used forphylogeny of organism Paralog genetic duplication occurs beforespeciation hence not suitable forphylogeny of organism45/6/02 Frank Olken - PGA PhylogenyTutorial7 Homoplasy Sequence similarity NOT due to commonancestry May arise due to parallelism or convergentevolution Parallelism Convergent evolution5/6/02 Frank Olken - PGA PhylogenyTutorial8 Phylogenetic tree Binary tree ( , fan-out from nodes = 2) Variously rooted or unrooted Tr

1 5/6/02 Frank Olken - PGA Phylogeny Tutorial 1 Phylogenetic Tree Computation Tutorial Frank Olken Lawrence Berkeley National Lab Presentation to PGA Course

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