Multiple Alignments and Phylogenies Mark Voorhies 3/31/2011 Mark - - PowerPoint PPT Presentation

▶
multiple alignments and phylogenies
SMART_READER_LITE
LIVE PREVIEW

Multiple Alignments and Phylogenies Mark Voorhies 3/31/2011 Mark - - PowerPoint PPT Presentation

Jan 18, 2023 162 likes •543 views

Multiple Alignments and Phylogenies Mark Voorhies 3/31/2011 Mark Voorhies Multiple Alignments and Phylogenies Review Computer lab notebook Dates Input/output/parameters Mark Voorhies Multiple Alignments and Phylogenies Review

slide-1
SLIDE 1

Multiple Alignments and Phylogenies

Mark Voorhies 3/31/2011

Mark Voorhies Multiple Alignments and Phylogenies

slide-2
SLIDE 2

Review

Computer “lab notebook”

Dates Input/output/parameters

Mark Voorhies Multiple Alignments and Phylogenies

slide-3
SLIDE 3

Review

Computer “lab notebook”

Dates Input/output/parameters (screenshots)

Mark Voorhies Multiple Alignments and Phylogenies

slide-4
SLIDE 4

Review

Computer “lab notebook”

Dates Input/output/parameters (screenshots) E-mail result synopses (e.g., to PI)

Mark Voorhies Multiple Alignments and Phylogenies

slide-5
SLIDE 5

Review

Computer “lab notebook”

Dates Input/output/parameters (screenshots) E-mail result synopses (e.g., to PI)

BLAST

Fast, heuristic local alignment with statistical foundation

Mark Voorhies Multiple Alignments and Phylogenies

slide-6
SLIDE 6

Review

Computer “lab notebook”

Dates Input/output/parameters (screenshots) E-mail result synopses (e.g., to PI)

BLAST

Fast, heuristic local alignment with statistical foundation Gosh, we should have saved our BLAST reports!

Mark Voorhies Multiple Alignments and Phylogenies

slide-7
SLIDE 7

Comprehending our BLAST results

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

Mark Voorhies Multiple Alignments and Phylogenies

slide-8
SLIDE 8

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-9
SLIDE 9

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

slide-10
SLIDE 10

Nomenclature

Homologs heritable elements with a common evolutionary

  • rigin.

Mark Voorhies Multiple Alignments and Phylogenies

slide-11
SLIDE 11

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

slide-12
SLIDE 12

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

slide-13
SLIDE 13

Nomenclature

Mark Voorhies Multiple Alignments and Phylogenies

slide-14
SLIDE 14

Nomenclature

Mark Voorhies Multiple Alignments and Phylogenies

slide-15
SLIDE 15

Generating a multiple alignment in CLUSTALX

Mark Voorhies Multiple Alignments and Phylogenies

slide-16
SLIDE 16

Generating a multiple alignment in CLUSTALX

Mark Voorhies Multiple Alignments and Phylogenies

slide-17
SLIDE 17

Evolution implies a self-consistent model

Distances (Pairwise relationships) Topology (Evolutionary history)

Mark Voorhies Multiple Alignments and Phylogenies

slide-18
SLIDE 18

Measure all pairwise distances by dynamic programming

Mark Voorhies Multiple Alignments and Phylogenies

slide-19
SLIDE 19

Measure all pairwise distances by dynamic programming

Mark Voorhies Multiple Alignments and Phylogenies

slide-20
SLIDE 20

Generate a guide tree by UPGMA

Mark Voorhies Multiple Alignments and Phylogenies

slide-21
SLIDE 21

Generate a guide tree by UPGMA

Mark Voorhies Multiple Alignments and Phylogenies

slide-22
SLIDE 22

Generate a guide tree by UPGMA

Mark Voorhies Multiple Alignments and Phylogenies

slide-23
SLIDE 23

Generate a guide tree by UPGMA

Mark Voorhies Multiple Alignments and Phylogenies

slide-24
SLIDE 24

Generate a guide tree by UPGMA

Mark Voorhies Multiple Alignments and Phylogenies

slide-25
SLIDE 25

Progressive alignment following the guide tree

Mark Voorhies Multiple Alignments and Phylogenies

slide-26
SLIDE 26

Progressive alignment following the guide tree

Mark Voorhies Multiple Alignments and Phylogenies

slide-27
SLIDE 27

Progressive alignment following the guide tree

Mark Voorhies Multiple Alignments and Phylogenies

slide-28
SLIDE 28

Measure distances directly from the alignment

Mark Voorhies Multiple Alignments and Phylogenies

slide-29
SLIDE 29

Generate neighbor-joining tree from new distances

Mark Voorhies Multiple Alignments and Phylogenies

slide-30
SLIDE 30

Generate neighbor-joining tree from new distances

Mark Voorhies Multiple Alignments and Phylogenies

slide-31
SLIDE 31

Generate neighbor-joining tree from new distances

Mark Voorhies Multiple Alignments and Phylogenies

slide-32
SLIDE 32

Generate bootstrap values from subsets of the alignment

Mark Voorhies Multiple Alignments and Phylogenies

slide-33
SLIDE 33

Generating a neighbor joining tree in CLUSTALX

Mark Voorhies Multiple Alignments and Phylogenies

slide-34
SLIDE 34

Viewing the alignment and tree in JALVIEW

Mark Voorhies Multiple Alignments and Phylogenies

slide-35
SLIDE 35

Related tools

Multiple Alignment

T-Coffee MUSCLE COBALT

Tree building

MrBayes (Bayesian MCMC) PhyML (maximum likelihood)

Mark Voorhies Multiple Alignments and Phylogenies

slide-36
SLIDE 36

Searching with PSI-BLAST

Mark Voorhies Multiple Alignments and Phylogenies

slide-37
SLIDE 37

Homework

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

Mark Voorhies Multiple Alignments and Phylogenies