Phylogenetic methods for taxonomic profiling Siavash Mirarab - PowerPoint PPT Presentation

Phylogenetic methods for taxonomic profiling Siavash Mirarab University of California at San Diego (UCSD) Joint work with Tandy Warnow, Nam-Phuong Nguyen, Mike Nute, Mihai Pop, and Bo Liu

Phylogeny reconstruction pipeline gene 1 ACTGCACACCG   ACTGCCCCCG   AATGCCCCCG   CTGCACACGG samples gene 2 CTGAGCATCG   CTGAGCTCG   ATGAGCTC   Sequencing CTGACACG gene 1000 CAGGCACGCACGAA   AGCCACGCCATA   Bioinformatic ATGGCACGCCTA   AGCTACCACGGAT processing 2

Phylogeny reconstruction pipeline Step 1: Multiple sequence alignment gene 1 gene 1 ACTGCACACCG   ACTGCACACCG   ACTGCCCCCG   ACTGC-CCCCG   MSA AATGCCCCCG   AATGC-CCCCG   CTGCACACGG -CTGCACACGG samples gene 2 gene 2 CTGAGCATCG   CTGAGCATCG   CTGAGCTCG   CTGAGC-TCG   MSA ATGAGCTC   ATGAGC-TC-   Sequencing CTGACACG CTGA-CAC-G gene 1000 gene 1000 CAGGCACGCACGAA   CAGGCACGCACGAA   AGCCACGCCATA   AGC-CACGC-CATA   MSA Bioinformatic ATGGCACGCCTA   ATGGCACGC-C-TA   AGCTACCACGGAT AGCTAC-CACGGAT processing 2

Phylogeny reconstruction pipeline Step 2: Species tree reconstruction Approach 1: Concatenation Orangutan Chimpanzee supermatrix Phylogeny gene 1 gene 2 gene 1000 inference ACTGCACACCG   CTGAGCATCG   CAGAGCACGCACGAA   ACTGC-CCCCG   CTGAGC-TCG   AGCA-CACGC-CATA   AATGC-CCCCG   ATGAGC-TC-   ATGAGCACGC-C-TA   Gorilla Human -CTGCACACGG CTGA-CAC-G AGC-TAC-CACGGAT Step 1: Multiple sequence alignment Approach 2: Summary methods Gene tree estimation gene 1 gene 1 ACTGCACACCG   ACTGCACACCG   Chimp Gorilla ACTGCCCCCG   ACTGC-CCCCG   gene 1 MSA AATGCCCCCG   AATGC-CCCCG   CTGCACACGG -CTGCACACGG Orangutan Chimpanzee samples Human Orang. gene 2 gene 2 Gorilla Chimp gene 2 CTGAGCATCG   CTGAGCATCG   Summary CTGAGCTCG   CTGAGC-TCG   MSA method ATGAGCTC   ATGAGC-TC-   Sequencing CTGACACG CTGA-CAC-G Human Orang. Gorilla Human gene 1000 Orang. Chimp gene 1000 gene 1000 CAGGCACGCACGAA   CAGGCACGCACGAA   Human Gorilla AGCCACGCCATA   AGC-CACGC-CATA   MSA Bioinformatic ATGGCACGCCTA   ATGGCACGC-C-TA   AGCTACCACGGAT AGCTAC-CACGGAT processing 2

Phylogeny reconstruction pipeline Step 2: Species tree reconstruction Approach 1: Concatenation Orangutan Chimpanzee supermatrix Phylogeny gene 1 gene 2 gene 1000 inference ACTGCACACCG   CTGAGCATCG   CAGAGCACGCACGAA   ACTGC-CCCCG   CTGAGC-TCG   AGCA-CACGC-CATA   AATGC-CCCCG   ATGAGC-TC-   ATGAGCACGC-C-TA   Gorilla Human -CTGCACACGG CTGA-CAC-G AGC-TAC-CACGGAT Step 1: Multiple sequence alignment Approach 2: Summary methods Gene tree estimation gene 1 gene 1 ACTGCACACCG   ACTGCACACCG   Chimp Gorilla ACTGCCCCCG   ACTGC-CCCCG   gene 1 MSA AATGCCCCCG   AATGC-CCCCG   CTGCACACGG -CTGCACACGG Orangutan Chimpanzee samples Human Orang. gene 2 gene 2 Gorilla Chimp gene 2 CTGAGCATCG   CTGAGCATCG   Summary CTGAGCTCG   CTGAGC-TCG   MSA method ATGAGCTC   ATGAGC-TC-   Sequencing CTGACACG CTGA-CAC-G Human Orang. Gorilla Human gene 1000 Orang. Chimp gene 1000 gene 1000 CAGGCACGCACGAA   CAGGCACGCACGAA   Human Gorilla AGCCACGCCATA   AGC-CACGC-CATA   MSA Bioinformatic ATGGCACGCCTA   ATGGCACGC-C-TA   AGCTACCACGGAT AGCTAC-CACGGAT processing TGGCACGCAACG ATGGCACGCTA ATGGCACGCA AGCTAACACGGAT ATGGCACGA 2

Phylogeny reconstruction pipeline Step 2: Species tree reconstruction Approach 1: Concatenation Orangutan Chimpanzee supermatrix Phylogeny gene 1 gene 2 gene 1000 inference ACTGCACACCG   CTGAGCATCG   CAGAGCACGCACGAA   ACTGC-CCCCG   CTGAGC-TCG   AGCA-CACGC-CATA   AATGC-CCCCG   ATGAGC-TC-   ATGAGCACGC-C-TA   Gorilla Human -CTGCACACGG CTGA-CAC-G AGC-TAC-CACGGAT Step 1: Multiple sequence alignment Approach 2: Summary methods Gene tree estimation gene 1 gene 1 ACTGCACACCG   ACTGCACACCG   Chimp Gorilla ACTGCCCCCG   ACTGC-CCCCG   gene 1 MSA AATGCCCCCG   AATGC-CCCCG   CTGCACACGG -CTGCACACGG Orangutan Chimpanzee samples Human Orang. gene 2 gene 2 Gorilla Chimp gene 2 CTGAGCATCG   CTGAGCATCG   Summary CTGAGCTCG   CTGAGC-TCG   MSA method ATGAGCTC   ATGAGC-TC-   Sequencing CTGACACG CTGA-CAC-G Human Orang. Gorilla Human gene 1000 Orang. Chimp gene 1000 gene 1000 CAGGCACGCACGAA   CAGGCACGCACGAA   Human Gorilla AGCCACGCCATA   AGC-CACGC-CATA   MSA Bioinformatic ATGGCACGCCTA   ATGGCACGC-C-TA   AGCTACCACGGAT AGCTAC-CACGGAT processing TGGCACGCAACG ATGGCACGCTA ATGGCACGCA AGCTAACACGGAT Step 3: Phylogenetic placement ATGGCACGA gene 1000 gene 200 gene 30 Gorilla Chimp Gorilla Chimp Gorilla Chimp CAGGCACGCACGAA   CAGGCACGCACGAA   CAGGCACGCACGAA   AGC-CACGC-CATA   AGC-CACGC-CATA   AGC-CACGC-CATA   ATGGCACGC-C-TA   ATGGCACGC-C-TA   ATGGCACGC-C-TA   Human Orang. Human Orang. AGCTAC-CACGGAT AGCTAC-CACGGAT AGCTAC-CACGGAT Human Orang. -ACATGGCT----- ----ATGGCGA--- -ACATGGCT----- -----CATTGCT-- 2

Phylogeny reconstruction pipeline Step 2: Species tree reconstruction — PASTA Approach 1: Concatenation Orangutan Chimpanzee — UPP supermatrix Phylogeny gene 1 gene 2 gene 1000 inference ACTGCACACCG   CTGAGCATCG   CAGAGCACGCACGAA   ACTGC-CCCCG   CTGAGC-TCG   AGCA-CACGC-CATA   AATGC-CCCCG   ATGAGC-TC-   ATGAGCACGC-C-TA   Gorilla Human -CTGCACACGG CTGA-CAC-G AGC-TAC-CACGGAT Step 1: Multiple sequence alignment Approach 2: Summary methods Gene tree estimation gene 1 gene 1 ACTGCACACCG   ACTGCACACCG   Chimp Gorilla ACTGCCCCCG   ACTGC-CCCCG   gene 1 MSA AATGCCCCCG   AATGC-CCCCG   CTGCACACGG -CTGCACACGG Orangutan Chimpanzee samples Human Orang. gene 2 gene 2 Gorilla Chimp gene 2 CTGAGCATCG   CTGAGCATCG   Summary CTGAGCTCG   CTGAGC-TCG   MSA method ATGAGCTC   ATGAGC-TC-   Sequencing CTGACACG CTGA-CAC-G Human Orang. Gorilla Human gene 1000 Orang. Chimp gene 1000 gene 1000 CAGGCACGCACGAA   CAGGCACGCACGAA   Human Gorilla AGCCACGCCATA   AGC-CACGC-CATA   MSA Bioinformatic ATGGCACGCCTA   ATGGCACGC-C-TA   AGCTACCACGGAT AGCTAC-CACGGAT processing TGGCACGCAACG ATGGCACGCTA ATGGCACGCA AGCTAACACGGAT Step 3: Phylogenetic placement ATGGCACGA gene 1000 gene 200 gene 30 Gorilla Chimp Gorilla Chimp Gorilla Chimp CAGGCACGCACGAA   CAGGCACGCACGAA   CAGGCACGCACGAA   AGC-CACGC-CATA   AGC-CACGC-CATA   AGC-CACGC-CATA   ATGGCACGC-C-TA   ATGGCACGC-C-TA   ATGGCACGC-C-TA   Human Orang. Human Orang. AGCTAC-CACGGAT AGCTAC-CACGGAT AGCTAC-CACGGAT Human Orang. -ACATGGCT----- ----ATGGCGA--- -ACATGGCT----- -----CATTGCT-- 2

Phylogeny reconstruction pipeline Step 2: Species tree reconstruction Sta$s$cal ¡ — PASTA Approach 1: Concatenation binning Orangutan Chimpanzee — UPP supermatrix Phylogeny gene 1 gene 2 gene 1000 inference ACTGCACACCG   CTGAGCATCG   CAGAGCACGCACGAA   ACTGC-CCCCG   CTGAGC-TCG   AGCA-CACGC-CATA   AATGC-CCCCG   ATGAGC-TC-   ATGAGCACGC-C-TA   Gorilla Human -CTGCACACGG CTGA-CAC-G AGC-TAC-CACGGAT Step 1: Multiple sequence alignment Approach 2: Summary methods Gene tree estimation gene 1 gene 1 ACTGCACACCG   ACTGCACACCG   Chimp Gorilla ACTGCCCCCG   ACTGC-CCCCG   gene 1 MSA AATGCCCCCG   AATGC-CCCCG   CTGCACACGG -CTGCACACGG Orangutan Chimpanzee samples Human Orang. gene 2 gene 2 Gorilla Chimp gene 2 CTGAGCATCG   CTGAGCATCG   Summary CTGAGCTCG   CTGAGC-TCG   MSA method ATGAGCTC   ATGAGC-TC-   Sequencing CTGACACG CTGA-CAC-G Human Orang. Gorilla Human gene 1000 Orang. Chimp gene 1000 gene 1000 ASTRAL CAGGCACGCACGAA   CAGGCACGCACGAA   Human Gorilla AGCCACGCCATA   AGC-CACGC-CATA   MSA Bioinformatic ATGGCACGCCTA   ATGGCACGC-C-TA   AGCTACCACGGAT AGCTAC-CACGGAT processing TGGCACGCAACG ATGGCACGCTA ATGGCACGCA AGCTAACACGGAT Step 3: Phylogenetic placement ATGGCACGA gene 1000 gene 200 gene 30 Gorilla Chimp Gorilla Chimp Gorilla Chimp CAGGCACGCACGAA   CAGGCACGCACGAA   CAGGCACGCACGAA   AGC-CACGC-CATA   AGC-CACGC-CATA   AGC-CACGC-CATA   ATGGCACGC-C-TA   ATGGCACGC-C-TA   ATGGCACGC-C-TA   Human Orang. Human Orang. AGCTAC-CACGGAT AGCTAC-CACGGAT AGCTAC-CACGGAT Human Orang. -ACATGGCT----- ----ATGGCGA--- -ACATGGCT----- -----CATTGCT-- 2

Phylogenetic methods for taxonomic profiling Siavash Mirarab - PowerPoint PPT Presentation

Phylogenetic methods for taxonomic profiling Siavash Mirarab University of California at San Diego (UCSD) Joint work with Tandy Warnow, Nam-Phuong Nguyen, Mike Nute, Mihai Pop, and Bo Liu Phylogeny reconstruction pipeline gene 1 ACTGCACACCG

Assessing Phylogenetic Hypotheses and Phylogenetic Data We use numerical phylogenetic methods

Phylogenetic Methods Multiple Sequence Alignment Pairwise distance matrix Clustering algorithms:

Comparison of commonly used methods for combining multiple phylogenetic data sets Anne Kupczok,

Morocco: a taxonomic and ecological study S. Sahib, P.Grootaert,B.Wakkie & B. Belqat 1 1 -

Inferring the Past: Phylogenetic Trees (chapter 12) The biological problem l Parsimony and

Phylogenetic Trees Distance trees Genome 373 Genomic Informatics Elhanan Borenstein A quick

Applying Phylogenetic Methods to Analyse Ancient Chinese Oracle-Bone Characters Related to

Analysis of Phylogenetic Tree Methods on Chloroplast Genes William Zhang Project Outline

Leaving no one behind The role of evidence-building and profiling to include displacement in

Balance indices for phylogenetic trees under well-known probability models Universitat de les

Profiling of Algorithms Profiling refers to the experimental measurement of the performance of

COZ : Finding Code that Counts with Causal Profiling Anuja Golechha Agenda Profiling

CSCE 471/871 Lecture 5: Building Phylogenetic Trees Building trees from pairwise distances

An introduction to Profiling Physics Coding Club: 09/06/2017 D. Dickinson

Is the best model good enough? Assessing the absolute fit of phylogenetic models via posterior

Profiling of Data-Parallel Processors Daniel Kruck 09/02/2014 09/02/2014 Profiling Daniel

Phylogenetic Trees in ACL2 Warren A. Hunt Jr. and Serita M. Nelesen The University of Texas at

Use of graphs and taxonomic classifications to analyze content relationships among courseware

Phylogenetic tree Michael Schroeder Biotechnology Center TU Dresden Phylogenetic trees

Phylogenetic tree Michael Schroeder Biotechnology Center TU Dresden Phylogenetic trees

On the proper use of phylogenetic information in typology Gerhard Jger Tbingen University

Web User Profiling using Data Redundancy http://aminer.org/profiling Xiaotao Gu, Hong Yang, Jie

Supplementary Material Impact of host DNA and sequencing depth on the taxonomic resolution of

Phylogenetic Networks Networks Phylogenetic Daniel H. Huson Daniel H. Huson www-

Phylogenetic methods for taxonomic profiling Siavash Mirarab - PowerPoint PPT Presentation

Phylogenetic methods for taxonomic profiling Siavash Mirarab University of California at San Diego (UCSD) Joint work with Tandy Warnow, Nam-Phuong Nguyen, Mike Nute, Mihai Pop, and Bo Liu Phylogeny reconstruction pipeline gene 1 ACTGCACACCG

Assessing Phylogenetic Hypotheses and Phylogenetic Data We use numerical phylogenetic methods

Phylogenetic Methods Multiple Sequence Alignment Pairwise distance matrix Clustering algorithms:

Comparison of commonly used methods for combining multiple phylogenetic data sets Anne Kupczok,

Morocco: a taxonomic and ecological study S. Sahib, P.Grootaert,B.Wakkie &amp; B. Belqat 1 1 -

Inferring the Past: Phylogenetic Trees (chapter 12) The biological problem l Parsimony and

Phylogenetic Trees Distance trees Genome 373 Genomic Informatics Elhanan Borenstein A quick

Applying Phylogenetic Methods to Analyse Ancient Chinese Oracle-Bone Characters Related to

Analysis of Phylogenetic Tree Methods on Chloroplast Genes William Zhang Project Outline

Leaving no one behind The role of evidence-building and profiling to include displacement in

Balance indices for phylogenetic trees under well-known probability models Universitat de les

Profiling of Algorithms Profiling refers to the experimental measurement of the performance of

COZ : Finding Code that Counts with Causal Profiling Anuja Golechha Agenda Profiling

CSCE 471/871 Lecture 5: Building Phylogenetic Trees Building trees from pairwise distances

An introduction to Profiling Physics Coding Club: 09/06/2017 D. Dickinson

Is the best model good enough? Assessing the absolute fit of phylogenetic models via posterior

Profiling of Data-Parallel Processors Daniel Kruck 09/02/2014 09/02/2014 Profiling Daniel

Phylogenetic Trees in ACL2 Warren A. Hunt Jr. and Serita M. Nelesen The University of Texas at

Use of graphs and taxonomic classifications to analyze content relationships among courseware

Phylogenetic tree Michael Schroeder Biotechnology Center TU Dresden Phylogenetic trees

Phylogenetic tree Michael Schroeder Biotechnology Center TU Dresden Phylogenetic trees

On the proper use of phylogenetic information in typology Gerhard Jger Tbingen University

Web User Profiling using Data Redundancy http://aminer.org/profiling Xiaotao Gu, Hong Yang, Jie

Supplementary Material Impact of host DNA and sequencing depth on the taxonomic resolution of

Phylogenetic Networks Networks Phylogenetic Daniel H. Huson Daniel H. Huson www-

Morocco: a taxonomic and ecological study S. Sahib, P.Grootaert,B.Wakkie & B. Belqat 1 1 -