Multiple Alignments and Phylogenies Mark Voorhies 3/29/2012 Mark - - PowerPoint PPT Presentation

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Multiple Alignments and Phylogenies Mark Voorhies 3/29/2012 Mark Voorhies Multiple Alignments and Phylogenies Comprehending our BLAST results We have a bunch of sequences that look similar to our query Mark Voorhies Multiple Alignments and

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Multiple Alignments and Phylogenies

Mark Voorhies 3/29/2012

Mark Voorhies Multiple Alignments and Phylogenies

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Comprehending our BLAST results

We have a bunch of sequences that look similar to our query

Mark Voorhies Multiple Alignments and Phylogenies

SLIDE 3

Comprehending our BLAST results

We have a bunch of sequences that look similar to our query We infer that they are homologous to each other

Mark Voorhies Multiple Alignments and Phylogenies

SLIDE 4

Comprehending our BLAST results

We have a bunch of sequences that look similar to our query We infer that they are homologous to each other What does that mean, anyway?

Mark Voorhies Multiple Alignments and Phylogenies

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Nomenclature

Homologs heritable elements with a common evolutionary

rigin.

Mark Voorhies Multiple Alignments and Phylogenies

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Nomenclature

Homologs heritable elements with a common evolutionary

rigin.

Orthologs homologs arising from speciation. Paralogs homologs arising from duplication and divergence within a single genome.

Mark Voorhies Multiple Alignments and Phylogenies

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Nomenclature

Homologs heritable elements with a common evolutionary

rigin.

Orthologs homologs arising from speciation. Paralogs homologs arising from duplication and divergence within a single genome. Xenologs homologs arising from horizontal transfer. Onologs homologs arising from whole genome duplication.

Mark Voorhies Multiple Alignments and Phylogenies

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Nomenclature

Mark Voorhies Multiple Alignments and Phylogenies

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Nomenclature

Mark Voorhies Multiple Alignments and Phylogenies

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Generating a multiple alignment in CLUSTALX

Mark Voorhies Multiple Alignments and Phylogenies

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Generating a multiple alignment in CLUSTALX

Mark Voorhies Multiple Alignments and Phylogenies

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Evolution implies a self-consistent model

Distances (Pairwise relationships) Topology (Evolutionary history)

Mark Voorhies Multiple Alignments and Phylogenies

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Measure all pairwise distances by dynamic programming

Mark Voorhies Multiple Alignments and Phylogenies

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Measure all pairwise distances by dynamic programming

Mark Voorhies Multiple Alignments and Phylogenies

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Generate a guide tree by UPGMA

Mark Voorhies Multiple Alignments and Phylogenies

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Generate a guide tree by UPGMA

Mark Voorhies Multiple Alignments and Phylogenies

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Generate a guide tree by UPGMA

Mark Voorhies Multiple Alignments and Phylogenies

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Generate a guide tree by UPGMA

Mark Voorhies Multiple Alignments and Phylogenies

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Generate a guide tree by UPGMA

Mark Voorhies Multiple Alignments and Phylogenies

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Progressive alignment following the guide tree

Mark Voorhies Multiple Alignments and Phylogenies

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Progressive alignment following the guide tree

Mark Voorhies Multiple Alignments and Phylogenies

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Progressive alignment following the guide tree

Mark Voorhies Multiple Alignments and Phylogenies

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Measure distances directly from the alignment

Mark Voorhies Multiple Alignments and Phylogenies

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Generate neighbor-joining tree from new distances

Mark Voorhies Multiple Alignments and Phylogenies

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Generate neighbor-joining tree from new distances

Mark Voorhies Multiple Alignments and Phylogenies

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Generate neighbor-joining tree from new distances

Mark Voorhies Multiple Alignments and Phylogenies

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Generate bootstrap values from subsets of the alignment

Mark Voorhies Multiple Alignments and Phylogenies

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Generating a neighbor joining tree in CLUSTALX

Mark Voorhies Multiple Alignments and Phylogenies

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Viewing the alignment and tree in JALVIEW

Mark Voorhies Multiple Alignments and Phylogenies

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Related tools

Multiple Alignment

T-Coffee MUSCLE COBALT

Tree building

MrBayes (Bayesian MCMC) PhyML (maximum likelihood)

Work benches

MESQUITE UGENE

Mark Voorhies Multiple Alignments and Phylogenies

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Searching with PSI-BLAST

Mark Voorhies Multiple Alignments and Phylogenies

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Homework

Play with CLUSTALX, JALVIEW, and PSI-BLAST Read PLoS Comp. Biol. 4:e1000069

Mark Voorhies Multiple Alignments and Phylogenies