Figure A1. Phylogenetic trees based on concatenated sequences of eight MLST loci. Phylogenetic trees were constructed based on concatenated sequences
|
|
- Stella Gilbert
- 5 years ago
- Views:
Transcription
1 A.
2 B.
3 Figure A1. Phylogenetic trees based on concatenated sequences of eight MLST loci. Phylogenetic trees were constructed based on concatenated sequences of eight housekeeping loci for 12 unique STs using Maximum-likelihood (A) and Neighbour-joining (B) methods. Individual strains and STs can be identified in the traditional rectangular branch style. Bootstrap support values of over 70% are shown.
4 A. ADK-4 ADK-3 ADK-1 ADK-2 ADK-4 ADK-3 ADK-1 ADK-2 VANTTGLFHLSTGDIFRTVMQEQGALSQTLAHYMNQGLYVPDELTNQTFWHFVTTHQNEL VANTTGLFHLSTGDIFRSVMQEQGALSQTLAHYMNQGLYVPDELTNQTFWHFVTTHQNEL VANTTGLFHLSTGDIFRSVMQEQGALSQTLAHYMNQGLYVPDELTNQTFWHFVTTHQNEL VANTTGLFHLSTGDIFRSVMQEQGALSQTLAHYMNQGLYVPDELTNQTFWHFVTTHQNEL *****************:****************************************** ADK-4 KPPLKANQCDRCHATLQARNDDTEAVILKRLTLYEDT 157 ADK-3 KPPLKANQCDLCHATLQARNDDTEAVILKRLTLYEDT 157 ADK-1 KPPLKANQCDRCHATLQARNDDTEAVILKRLTLYEDT 157 ADK-2 KPPLKANQCDRCHAMLQARNDDTEAVILKRLTLYEDT 157 ********** *** ********************** B. ARCC-1 ARCC-2 ARCC-1 ARCC-2 ARCC-1 ARCC-2 PHQAVYFLTQTLVEASDPAFQNPNKPVGPFYNTEETARSANPNSTVVEDAGRGWRKVVAS PHQAVYFLTQTLVEASDPAFQNPNKPVGPFYNTEETARSANPNSTVVEDAGRGWRKVVAS PKPVDVLGIDAIKSSFNQGNLVIVGGGGGVPTIKTKSGYATVDGVIDKDLALSEIAIKVE PKPVDVLGIDAIKSSFNQGNLVIVGGGGGVPTIKTKSGYATVDGVIDKDLALSEIAIKVE ADLFVILTAVDFVYINYGQPNEQKLTCINTKEAKTLMAANQFAKGSMLPKVEACLNFVQS ADLFVILTAVDFVYINYGQPNEQKLTCINTKEAKTLMAANQFAKGSMLPKVEACLNFVQS ARCC-1 GTNKTAIIAQ 190 ARCC-2 GTNKTAIIAQ 190 ********** C. GLYA-1 GLYA-3 GLYA-2 GLYA-1 GLYA-3 GLYA-2 GLYA-1 GLYA-3 GLYA-2 ENYVSRDILEVTGSILTNKYAEGYPTRRFYEGCEVVDESESLAINTCKELFGAKWANVQP ENYVSRDILEVTGSILTNKYAEGYPTRRFYEGCEVVDESESLAINTCKELFGAKWANVQP ENYVSRDILEVTGSILTNKYAEGYPTRRFYEGCEVVDESESLAINTCKELFGAKWANVQP HSGSSANYAVYLALLKPGDAILGLDLNCGGHLTHGNKFNFSGKQYQPYSYTINPETEMLD HSGSSANYAVYLALLKPGDAILGLDLNCGGHLTHGNKFNFSGKQYQPYSYTINPETEMLD HSGSSANYAVYLALLKPGDAILGLDLNCGGHLTHGNKFNFSGKQYQPYSYTINPETEMLD YDEVLRVAREVKPKLIICGFSNYSRTVDFERFSAIAKEVGAYLLADIAHIAGLVAAGLHP YDEVLRVAREVKPKLIICGFSNYSRTVDFERFSAIAKEVGAYLLADIAHIAGLVAAGLHP YDEVLRVAREVKPKLIICGFSNYSRTVDFERFSAIAKEVGAYLLADIAHIAGLVAAGLHP GLYA-1 NPLPYTDVVTSTTHKTLRGPRGGLIMSNNEAIIRKLDSGVFPGC 224 GLYA-3 NPLPYTDVVTSTTHKTLRGPRGGLIMSNNEAIIRKLDSGVFPGC 224 GLYA-2 NPLPYADVVTSTTHKTLRGPRGGLIMSNNEAIIRKLDSGVFPGC 224 *****:**************************************
5 D. VTDSMKYTTVVCATASNPASMIYLTPFTGITIAEYWLKQGKDVLIVFDDLSKHAIAYRTL VTDSMKYTTVVCATASNPASMIYLTPFTGITIAEYWLKQGKDVLIVFDDLSKHAIAYRTL VTDSMKYTTVVCATASDPASMIYLTPFTGITIAEYWLKQGKDVLIVFDDLSKHAIAYRTL VTDSMKYTTVVCATASDPASMIYLTPFTGITIAEYWLKQGKDVLIVFDDLSKHAIAYRTL ****************:******************************************* SLLLRRPPGREAFPGDVFYLHSRLL 265 SLLLRRPPGREAFPGDVFYLHSRLL 265 SLLLRRPPGREAFPGDVFYLHSRLL 265 SLLLRRPPGREAFPGDVFYLHSRLL 265 ************************* E. GMK-1 GMK-2 GMK-1 GMK-2 SGVGKSSLVRCLIDHFKDKLRYSISATTRKMRNSETEGVDYFFKDKAEFEKLIAADAFVE SGVGKSSLVRCLIDHFKDKLRYSISATTRKMRNSETEGVDYFFKDKAEFEKLIAADAFVE WAMYNDNYYGTLKSQAEQIIHNGGNLVLEIEYQGALQVKQKYPNDVVLIFIKPPSMEELL WAMYNDNYYGTLKSQAEQIIHNGGNLVLEIEYQGALQVKQKYPNDVVLIFIKPPSMEELL GMK-1 VRLKKRNDEDA 131 GMK-2 VRLKKRNDEDA 131 *********** F. GYRB-1 GYRB-2 GYRB-1 GYRB-2 VPDFTVMEKSDYKQTVIASRLQQLAFLNKGIQIDFVDERRQNPQSFSWKYDGGLVQYIHH VPDFTVMEKSDYKQTVIASRLQQLAFLNKGIQIDFVDERRQNPQSFSWKYDGGLVQYIHH LNNEKEPLFEDIIFGEKTDTVKSVSRDESYTIKVEVAFQYNKTYNQSIFSFCNNINTTEG LNNEKEPLFEDIIFGEKTDTVKSVSRDESYTIKVEVAFQYNKTYNQSIFSFCNNINTTEG GYRB-1 GTHVEGFRNALVKIINRFAVEN 142 GYRB-2 GTHVEGFRNALVKIINRFAVEN 142 **********************
6 G. H. APCTMKSDLEAFMVFLKDYHNVIIGTLGGRYYGMDRDQRWDREEIAYNAILGNSKASFTD APCTMKSDLEAFMVFLKDYHNVIIGTLGGRYYGMDRDQRWDREEIAYNAILGNSKASFTD APCTMKSDLEAFMVFLKDYHNVIIGTLGGRYYGMDRDQRWDREEIAYNAILGNSKASFTD PVAYVQSAYDQKVTDEFLYPAVNGNVDKEQFALKDHDSVIFFNFRPDRARQMSHMLFQTD PVAYVQSAYDQKVTDEFLYPAVNGNVDKEQFALKDHDSVIFFNFRPDRARQMSHMLFQTD PVAYVQSAYDQKVTDEFLYPAVNGNVDKEQFALKDHDSVIFFNFRPDRARQMSHMLFQTD YYDYTPKAGRKHNLFFVTMMNYEGIKPSAVVFPPETIPNTFGEVIAHNKLKQLRIAETEK YYDYTPKAGRKYNLFFVTMMNYEGIKPSAVVFPPETIPNTFGEVIAHNKLKQLRIAETEK YYDYTPKAGRKHNLFFVTMMNYEGIKPSAVVFPPETIPNTFGEVIAHNKLKQLRIAETEK ***********:************************************************ YAHVTFFFDGGVEVDLPNETKCMVPSLKVATYDLAPEMACKGITDQLLNQINQFDLTVLN YAHVTFFFDGGVEVDLPNETKCMVPSLKVATYDLAPEMACKGITDQLLNQINQFDLTVLN YAHVTFFFDGGVEVDLPNETKCMVPSLKVATYDLAPEMACKGITDQLLNQINQFDLTVLN FANPDMVGHTGNYAACVQGLEALDVQIQRIIDFCKANHITLFLTADHGNAEEMIDSNNNP FANPDMVGHTGNYAACVQGLEALDVQIQRIIDFCKANHITLFLTADHGNAEEMIDSNNNP FANPDMVGHTGNYAACVQGLEALDVQIQRIIDFCKANHITLFLTADHGNAEEMIDSNNNP VTKHTVNKVPFVCTDTNIDLQQDSASLANIAPTILAYLGLKQPAEMTANSLLYKKV VTKHTVNKVPFVCTDTNIDLQQDSASLANIAPTILAYLGLKQPAEMTANSLLISKK VTKHTVNKVPFVCTDTNIDLQQDSASLANIAPTILAYLGLKQPAEMTANSLLISKK ****************************************************.* PPA-1 PPA-2 IFADQAFLPGVVVPTRIVGALEMVDDGELDTKLLGVIDCDPRYKEINSVNDLPKHRVDEI IFADQAFLPGVVVPTRIVGALEMVDDGELDTKLLGVIDCDPRYKEINSVNDLPKHRVDEI PPA-1 PPA-2 IGFLKTYKLLQKKEVIIKGVQSLEW IGFFKTYKLLQKKEVIIKGVQSLEW ***:********************* Figure A2. Alignments of amino acid sequences of each allelic type at each of the eight MLST loci. Amino acid sequence alignments were generated for each of the eight loci based on nucleotide sequence of each allelic type. Synonomous changes in amino acid sequence are highlighted in yellow. * (asterix) indicates positions which have a single, fully conserved residue; : (colon) indicates conservation between groups of strongly similar properties - scoring > 0.5 in the Gonnet PAM 250 matrix;. (period) indicates conservation between groups of weakly similar properties - scoring < 0.5 in the Gonnet PAM 250 matrix.
Bioinformatics. Scoring Matrices. David Gilbert Bioinformatics Research Centre
Bioinformatics Scoring Matrices David Gilbert Bioinformatics Research Centre www.brc.dcs.gla.ac.uk Department of Computing Science, University of Glasgow Learning Objectives To explain the requirement
More informationTHEORY. Based on sequence Length According to the length of sequence being compared it is of following two types
Exp 11- THEORY Sequence Alignment is a process of aligning two sequences to achieve maximum levels of identity between them. This help to derive functional, structural and evolutionary relationships between
More informationPhylogenetic analyses. Kirsi Kostamo
Phylogenetic analyses Kirsi Kostamo The aim: To construct a visual representation (a tree) to describe the assumed evolution occurring between and among different groups (individuals, populations, species,
More informationQuantifying sequence similarity
Quantifying sequence similarity Bas E. Dutilh Systems Biology: Bioinformatic Data Analysis Utrecht University, February 16 th 2016 After this lecture, you can define homology, similarity, and identity
More informationConstructing Evolutionary/Phylogenetic Trees
Constructing Evolutionary/Phylogenetic Trees 2 broad categories: Distance-based methods Ultrametric Additive: UPGMA Transformed Distance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood
More informationPOPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics
POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics - in deriving a phylogeny our goal is simply to reconstruct the historical relationships between a group of taxa. - before we review the
More informationSequence Bioinformatics. Multiple Sequence Alignment Waqas Nasir
Sequence Bioinformatics Multiple Sequence Alignment Waqas Nasir 2010-11-12 Multiple Sequence Alignment One amino acid plays coy; a pair of homologous sequences whisper; many aligned sequences shout out
More informationConstructing Evolutionary/Phylogenetic Trees
Constructing Evolutionary/Phylogenetic Trees 2 broad categories: istance-based methods Ultrametric Additive: UPGMA Transformed istance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood
More informationComparison of 61 E. coli genomes
Comparison of 61 E. coli genomes Center for Biological Sequence Analysis Department of Systems Biology Dave Ussery! DTU course 27105 - Comparative Genomics Oksana s 61 E. coli genomes paper! Monday, 23
More informationProcesses of Evolution
15 Processes of Evolution Forces of Evolution Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive Natural selection can act on quantitative traits in three ways: Stabilizing selection
More informationSUPPLEMENTARY INFORMATION
Supplementary information S3 (box) Methods Methods Genome weighting The currently available collection of archaeal and bacterial genomes has a highly biased distribution of isolates across taxa. For example,
More informationMOLECULAR PHYLOGENY AND GENETIC DIVERSITY ANALYSIS. Masatoshi Nei"
MOLECULAR PHYLOGENY AND GENETIC DIVERSITY ANALYSIS Masatoshi Nei" Abstract: Phylogenetic trees: Recent advances in statistical methods for phylogenetic reconstruction and genetic diversity analysis were
More informationTree of Life iological Sequence nalysis Chapter http://tolweb.org/tree/ Phylogenetic Prediction ll organisms on Earth have a common ancestor. ll species are related. The relationship is called a phylogeny
More informationSequence Alignment: Scoring Schemes. COMP 571 Luay Nakhleh, Rice University
Sequence Alignment: Scoring Schemes COMP 571 Luay Nakhleh, Rice University Scoring Schemes Recall that an alignment score is aimed at providing a scale to measure the degree of similarity (or difference)
More informationPhylogenetics: Bayesian Phylogenetic Analysis. COMP Spring 2015 Luay Nakhleh, Rice University
Phylogenetics: Bayesian Phylogenetic Analysis COMP 571 - Spring 2015 Luay Nakhleh, Rice University Bayes Rule P(X = x Y = y) = P(X = x, Y = y) P(Y = y) = P(X = x)p(y = y X = x) P x P(X = x 0 )P(Y = y X
More informationAlgorithms in Bioinformatics FOUR Pairwise Sequence Alignment. Pairwise Sequence Alignment. Convention: DNA Sequences 5. Sequence Alignment
Algorithms in Bioinformatics FOUR Sami Khuri Department of Computer Science San José State University Pairwise Sequence Alignment Homology Similarity Global string alignment Local string alignment Dot
More informationAmira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut
Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic analysis Phylogenetic Basics: Biological
More informationDNA Phylogeny. Signals and Systems in Biology Kushal EE, IIT Delhi
DNA Phylogeny Signals and Systems in Biology Kushal Shah @ EE, IIT Delhi Phylogenetics Grouping and Division of organisms Keeps changing with time Splitting, hybridization and termination Cladistics :
More informationSara C. Madeira. Universidade da Beira Interior. (Thanks to Ana Teresa Freitas, IST for useful resources on this subject)
Bioinformática Sequence Alignment Pairwise Sequence Alignment Universidade da Beira Interior (Thanks to Ana Teresa Freitas, IST for useful resources on this subject) 1 16/3/29 & 23/3/29 27/4/29 Outline
More informationNJMerge: A generic technique for scaling phylogeny estimation methods and its application to species trees
NJMerge: A generic technique for scaling phylogeny estimation methods and its application to species trees Erin Molloy and Tandy Warnow {emolloy2, warnow}@illinois.edu University of Illinois at Urbana
More informationBasics on bioinforma-cs Lecture 7. Nunzio D Agostino
Basics on bioinforma-cs Lecture 7 Nunzio D Agostino nunzio.dagostino@entecra.it; nunzio.dagostino@gmail.com Multiple alignments One sequence plays coy a pair of homologous sequence whisper many aligned
More informationFIG S1: Plot of rarefaction curves for Borrelia garinii Clp A allelic richness for questing Ixodes
FIG S1: Plot of rarefaction curves for Borrelia garinii Clp A allelic richness for questing Ixodes ricinus sampled in continental Europe, England, Scotland and grey squirrels (Sciurus carolinensis) from
More informationSequence Alignments. Dynamic programming approaches, scoring, and significance. Lucy Skrabanek ICB, WMC January 31, 2013
Sequence Alignments Dynamic programming approaches, scoring, and significance Lucy Skrabanek ICB, WMC January 31, 213 Sequence alignment Compare two (or more) sequences to: Find regions of conservation
More informationIntraspecific gene genealogies: trees grafting into networks
Intraspecific gene genealogies: trees grafting into networks by David Posada & Keith A. Crandall Kessy Abarenkov Tartu, 2004 Article describes: Population genetics principles Intraspecific genetic variation
More informationDr. Amira A. AL-Hosary
Phylogenetic analysis Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic Basics: Biological
More informationA bioinformatics approach to the structural and functional analysis of the glycogen phosphorylase protein family
A bioinformatics approach to the structural and functional analysis of the glycogen phosphorylase protein family Jieming Shen 1,2 and Hugh B. Nicholas, Jr. 3 1 Bioengineering and Bioinformatics Summer
More information2 Genome evolution: gene fusion versus gene fission
2 Genome evolution: gene fusion versus gene fission Berend Snel, Peer Bork and Martijn A. Huynen Trends in Genetics 16 (2000) 9-11 13 Chapter 2 Introduction With the advent of complete genome sequencing,
More information08/21/2017 BLAST. Multiple Sequence Alignments: Clustal Omega
BLAST Multiple Sequence Alignments: Clustal Omega What does basic BLAST do (e.g. what is input sequence and how does BLAST look for matches?) Susan Parrish McDaniel College Multiple Sequence Alignments
More informationSupplementary Information for Hurst et al.: Causes of trends of amino acid gain and loss
Supplementary Information for Hurst et al.: Causes of trends of amino acid gain and loss Methods Identification of orthologues, alignment and evolutionary distances A preliminary set of orthologues was
More information7. Tests for selection
Sequence analysis and genomics 7. Tests for selection Dr. Katja Nowick Group leader TFome and Transcriptome Evolution Bioinformatics group Paul-Flechsig-Institute for Brain Research www. nowicklab.info
More informationA (short) introduction to phylogenetics
A (short) introduction to phylogenetics Thibaut Jombart, Marie-Pauline Beugin MRC Centre for Outbreak Analysis and Modelling Imperial College London Genetic data analysis with PR Statistics, Millport Field
More informationBINF6201/8201. Molecular phylogenetic methods
BINF60/80 Molecular phylogenetic methods 0-7-06 Phylogenetics Ø According to the evolutionary theory, all life forms on this planet are related to one another by descent. Ø Traditionally, phylogenetics
More informationConsensus methods. Strict consensus methods
Consensus methods A consensus tree is a summary of the agreement among a set of fundamental trees There are many consensus methods that differ in: 1. the kind of agreement 2. the level of agreement Consensus
More informationconcentration ( mol l -1 )
concentration ( mol l -1 ) 8 10 0 20 40 60 80 100 120 140 160 180 methane sulfide ammonium oxygen sulfate (/10) b depth (m) 12 14 Supplementary Figure 1. Water column parameters from August 2011. Chemical
More informationPhylogene)cs. IMBB 2016 BecA- ILRI Hub, Nairobi May 9 20, Joyce Nzioki
Phylogene)cs IMBB 2016 BecA- ILRI Hub, Nairobi May 9 20, 2016 Joyce Nzioki Phylogenetics The study of evolutionary relatedness of organisms. Derived from two Greek words:» Phle/Phylon: Tribe/Race» Genetikos:
More informationSupporting Information
Supporting Information Das et al. 10.1073/pnas.1302500110 < SP >< LRRNT > < LRR1 > < LRRV1 > < LRRV2 Pm-VLRC M G F V V A L L V L G A W C G S C S A Q - R Q R A C V E A G K S D V C I C S S A T D S S P E
More informationPhylogenetic Analysis. Han Liang, Ph.D. Assistant Professor of Bioinformatics and Computational Biology UT MD Anderson Cancer Center
Phylogenetic Analysis Han Liang, Ph.D. Assistant Professor of Bioinformatics and Computational Biology UT MD Anderson Cancer Center Outline Basic Concepts Tree Construction Methods Distance-based methods
More informationHow to read and make phylogenetic trees Zuzana Starostová
How to read and make phylogenetic trees Zuzana Starostová How to make phylogenetic trees? Workflow: obtain DNA sequence quality check sequence alignment calculating genetic distances phylogeny estimation
More informationStepping stones towards a new electronic prokaryotic taxonomy. The ultimate goal in taxonomy. Pragmatic towards diagnostics
Stepping stones towards a new electronic prokaryotic taxonomy - MLSA - Dirk Gevers Different needs for taxonomy Describe bio-diversity Understand evolution of life Epidemiology Diagnostics Biosafety...
More informationLecture 8 Multiple Alignment and Phylogeny
Introduction to Bioinformatics for Medical Research Gideon Greenspan gdg@cs.technion.ac.il Lecture 8 Multiple Alignment and Phylogeny Multiple Alignment & Phylogeny Multiple Alignment Scoring Complexity
More informationInferring phylogeny. Constructing phylogenetic trees. Tõnu Margus. Bioinformatics MTAT
Inferring phylogeny Constructing phylogenetic trees Tõnu Margus Contents What is phylogeny? How/why it is possible to infer it? Representing evolutionary relationships on trees What type questions questions
More informationSequence Based Bioinformatics
Structural and Functional Analysis of Inosine Monophosphate Dehydrogenase using Sequence-Based Bioinformatics Barry Sexton 1,2 and Troy Wymore 3 1 Bioengineering and Bioinformatics Summer Institute, Department
More informationBioinformatics 1. Sepp Hochreiter. Biology, Sequences, Phylogenetics Part 4. Bioinformatics 1: Biology, Sequences, Phylogenetics
Bioinformatics 1 Biology, Sequences, Phylogenetics Part 4 Sepp Hochreiter Klausur Mo. 30.01.2011 Zeit: 15:30 17:00 Raum: HS14 Anmeldung Kusss Contents Methods and Bootstrapping of Maximum Methods Methods
More informationSubstitution matrices
Introduction to Bioinformatics Substitution matrices Jacques van Helden Jacques.van-Helden@univ-amu.fr Université d Aix-Marseille, France Lab. Technological Advances for Genomics and Clinics (TAGC, INSERM
More informationThe Phylogenetic Handbook
The Phylogenetic Handbook A Practical Approach to DNA and Protein Phylogeny Edited by Marco Salemi University of California, Irvine and Katholieke Universiteit Leuven, Belgium and Anne-Mieke Vandamme Rega
More informationSequence Analysis 17: lecture 5. Substitution matrices Multiple sequence alignment
Sequence Analysis 17: lecture 5 Substitution matrices Multiple sequence alignment Substitution matrices Used to score aligned positions, usually of amino acids. Expressed as the log-likelihood ratio of
More information3.1: Place of collection of entomopathogenic nematode isolates : Measurement of 12 bacterial isolates 45
List of Tables 3.1: Place of collection of entomopathogenic nematode isolates... 39 3.2: Measurement of 12 bacterial isolates 45 3.3: Colony morphology of bacteria on nutrient agar 46 3.4: Colony morphology
More informationBioinformatics 1 -- lecture 9. Phylogenetic trees Distance-based tree building Parsimony
ioinformatics -- lecture 9 Phylogenetic trees istance-based tree building Parsimony (,(,(,))) rees can be represented in "parenthesis notation". Each set of parentheses represents a branch-point (bifurcation),
More informationMolecular Evolution & Phylogenetics
Molecular Evolution & Phylogenetics Heuristics based on tree alterations, maximum likelihood, Bayesian methods, statistical confidence measures Jean-Baka Domelevo Entfellner Learning Objectives know basic
More informationEvaluation Measures of Multiple Sequence Alignments. Gaston H. Gonnet, *Chantal Korostensky and Steve Benner. Institute for Scientic Computing
Evaluation Measures of Multiple Sequence Alignments Gaston H. Gonnet, *Chantal Korostensky and Steve Benner Institute for Scientic Computing ETH Zurich, 8092 Zuerich, Switzerland phone: ++41 1 632 74 79
More informationC3020 Molecular Evolution. Exercises #3: Phylogenetics
C3020 Molecular Evolution Exercises #3: Phylogenetics Consider the following sequences for five taxa 1-5 and the known outgroup O, which has the ancestral states (note that sequence 3 has changed from
More informationAdditional file 10. Classification of Pac sequences based on maximum-likelihood (ML) phylogenetic analyses. Analyses were performed on the same
Additional file 10. Classification of Pac sequences based on maximum-likelihood (ML) phylogenetic analyses. Analyses were performed on the same dataset alignments used for crucial Neighbor-joining trees
More informationScoring Matrices. Shifra Ben-Dor Irit Orr
Scoring Matrices Shifra Ben-Dor Irit Orr Scoring matrices Sequence alignment and database searching programs compare sequences to each other as a series of characters. All algorithms (programs) for comparison
More informationA Contribution to the Phylogeny of the Ciidae and its Relationships with Other Cucujoid and Tenebrionoid Beetles (Coleoptera: Cucujiformia)
Arthropod Systematics & Phylogeny I 66 (2) Electronic Supplement Museum für Tierkunde Dresden, ISSN 1863-7221, 5.12.2008 A Contribution to the Phylogeny of the Ciidae and its Relationships with Other Cucujoid
More informationPhylogenetic Trees. What They Are Why We Do It & How To Do It. Presented by Amy Harris Dr Brad Morantz
Phylogenetic Trees What They Are Why We Do It & How To Do It Presented by Amy Harris Dr Brad Morantz Overview What is a phylogenetic tree Why do we do it How do we do it Methods and programs Parallels
More informationPhylogeny: building the tree of life
Phylogeny: building the tree of life Dr. Fayyaz ul Amir Afsar Minhas Department of Computer and Information Sciences Pakistan Institute of Engineering & Applied Sciences PO Nilore, Islamabad, Pakistan
More informationSUPPLEMENTARY TABLES Table S1 Gene Primer Sequence Position (Size)
SUPPLEMENTARY TABLES Table S1 Primers used for gdna and mrna analyses Gene Primer Sequence Position (Size) mga F: 5 -TGGTTATATTACAATCTGGTACCATC 198-405 (208) R: 5 -GGTATGCGTCAAATAGGCATTGG emm23 F: 5'-GCTTTGACAGTTTTAGGGACAGG
More informationPhylogenetics: Building Phylogenetic Trees
1 Phylogenetics: Building Phylogenetic Trees COMP 571 Luay Nakhleh, Rice University 2 Four Questions Need to be Answered What data should we use? Which method should we use? Which evolutionary model should
More informationExample questions. Z:\summer_10_teaching\bioinfo\Beispiel_frage_bioinformatik.doc [1 / 5]
Example questions for Bioinformatics, first semester half Sommersemester 00 ote The schriftliche Klausur wurde auf deutsch geschrieben The questions will be based on material from the Übungen and the Lectures.
More informationSupporting Information
Supporting Information Ziemert et al. 10.1073/pnas.1324161111 Fig. S1. Geographic origin and numbers of Salinispora strains used in this study. Fig. S2. Operational biosynthetic unit (OBU) phylogeny supports
More informationAlgorithmic Methods Well-defined methodology Tree reconstruction those that are well-defined enough to be carried out by a computer. Felsenstein 2004,
Tracing the Evolution of Numerical Phylogenetics: History, Philosophy, and Significance Adam W. Ferguson Phylogenetic Systematics 26 January 2009 Inferring Phylogenies Historical endeavor Darwin- 1837
More informationLecture 4: Evolutionary Models and Substitution Matrices (PAM and BLOSUM)
Bioinformatics II Probability and Statistics Universität Zürich and ETH Zürich Spring Semester 2009 Lecture 4: Evolutionary Models and Substitution Matrices (PAM and BLOSUM) Dr Fraser Daly adapted from
More informationSome of these slides have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks!
Some of these slides have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks! Paul has many great tools for teaching phylogenetics at his web site: http://hydrodictyon.eeb.uconn.edu/people/plewis
More informationMidterm Exam #1. MB 451 Microbial Diversity. Honor pledge: I have neither given nor received unauthorized aid on this test.
Midterm xam #1 M 451 Microbial iversity Honor pledge: I have neither given nor received unauthorized aid on this test. Signed : ate : Feb 5, 2007 Name : KY 1. What are the three primary evolutionary branches
More informationSequence Alignment: A General Overview. COMP Fall 2010 Luay Nakhleh, Rice University
Sequence Alignment: A General Overview COMP 571 - Fall 2010 Luay Nakhleh, Rice University Life through Evolution All living organisms are related to each other through evolution This means: any pair of
More informationPhylogenetics: Building Phylogenetic Trees. COMP Fall 2010 Luay Nakhleh, Rice University
Phylogenetics: Building Phylogenetic Trees COMP 571 - Fall 2010 Luay Nakhleh, Rice University Four Questions Need to be Answered What data should we use? Which method should we use? Which evolutionary
More informationSex and virulence in Escherichia coli: an evolutionary perspective
Blackwell Publishing LtdOxford, UKMMIMolecular Microbiology0950-382X; Journal compilation 2006 Blackwell Publishing Ltd? 2006?? Original ArticleSex and virulencet. Wirth et al. Molecular Microbiology (2006)
More informationC.DARWIN ( )
C.DARWIN (1809-1882) LAMARCK Each evolutionary lineage has evolved, transforming itself, from a ancestor appeared by spontaneous generation DARWIN All organisms are historically interconnected. Their relationships
More informationLecture 22: Signatures of Selection and Introduction to Linkage Disequilibrium. November 12, 2012
Lecture 22: Signatures of Selection and Introduction to Linkage Disequilibrium November 12, 2012 Last Time Sequence data and quantification of variation Infinite sites model Nucleotide diversity (π) Sequence-based
More informationFirst generation sequencing and pairwise alignment (High-tech, not high throughput) Analysis of Biological Sequences
First generation sequencing and pairwise alignment (High-tech, not high throughput) Analysis of Biological Sequences 140.638 where do sequences come from? DNA is not hard to extract (getting DNA from a
More information"Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky
MOLECULAR PHYLOGENY "Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky EVOLUTION - theory that groups of organisms change over time so that descendeants differ structurally
More informationCoculture of two Developmental Stages of a Marine-derived Aspergillus alliaceus. Results in the Production of the Cytotoxic Bianthrone Allianthrone A
Coculture of two Developmental Stages of a Marine-derived Aspergillus alliaceus Results in the Production of the Cytotoxic Bianthrone Allianthrone A P. E. Mandelare, D. A. Adpressa, E. N. Kaweesa, L. N.
More informationPhylogenetic and Comparative Sequence Analysis of Thermostable Alpha Amylases of kingdom Archea, Prokaryotes and Eukaryotes
www.bioinformation.net Hypothesis Volume 10(7) Phylogenetic and Comparative Sequence Analysis of Thermostable Alpha Amylases of kingdom Archea, Prokaryotes and Eukaryotes Tayyaba Huma 1 *, Arooma Maryam
More informationBIOINFORMATICS LAB AP BIOLOGY
BIOINFORMATICS LAB AP BIOLOGY Bioinformatics is the science of collecting and analyzing complex biological data. Bioinformatics combines computer science, statistics and biology to allow scientists to
More informationSupporting Text 1. Comparison of GRoSS sequence alignment to HMM-HMM and GPCRDB
Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications, Cvicek et al. Supporting Text 1 Here we compare the GRoSS alignment
More informationMichael Yaffe Lecture #5 (((A,B)C)D) Database Searching & Molecular Phylogenetics A B C D B C D
7.91 Lecture #5 Database Searching & Molecular Phylogenetics Michael Yaffe B C D B C D (((,B)C)D) Outline Distance Matrix Methods Neighbor-Joining Method and Related Neighbor Methods Maximum Likelihood
More informationSupplementary Information
Supplementary Information Supplementary Figure 1. Schematic pipeline for single-cell genome assembly, cleaning and annotation. a. The assembly process was optimized to account for multiple cells putatively
More informationEvaluating phylogenetic hypotheses
Evaluating phylogenetic hypotheses Methods for evaluating topologies Topological comparisons: e.g., parametric bootstrapping, constrained searches Methods for evaluating nodes Resampling techniques: bootstrapping,
More informationaP. Short title: Mulberry badnavirus 1, a new species in the Badnavirus genus (e.g. 6 new species in the genus Zetavirus) Modules attached
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the
More informationHonor pledge: I have neither given nor received unauthorized aid on this test. Name :
Midterm Exam #1 MB 451 : Microbial Diversity Honor pledge: I have neither given nor received unauthorized aid on this test. Signed : Date : Name : 1. What are the three primary evolutionary branches of
More informationMultiple Sequence Alignments
Multiple Sequence Alignments...... Elements of Bioinformatics Spring, 2003 Tom Carter http://astarte.csustan.edu/ tom/ March, 2003 1 Sequence Alignments Often, we would like to make direct comparisons
More informationInDel 3-5. InDel 8-9. InDel 3-5. InDel 8-9. InDel InDel 8-9
Lecture 5 Alignment I. Introduction. For sequence data, the process of generating an alignment establishes positional homologies; that is, alignment provides the identification of homologous phylogenetic
More informationBLAST. Varieties of BLAST
BLAST Basic Local Alignment Search Tool (1990) Altschul, Gish, Miller, Myers, & Lipman Uses short-cuts or heuristics to improve search speed Like speed-reading, does not examine every nucleotide of database
More informationAnatomy of a species tree
Anatomy of a species tree T 1 Size of current and ancestral Populations (N) N Confidence in branches of species tree t/2n = 1 coalescent unit T 2 Branch lengths and divergence times of species & populations
More informationPage 1. Evolutionary Trees. Why build evolutionary tree? Outline
Page Evolutionary Trees Russ. ltman MI S 7 Outline. Why build evolutionary trees?. istance-based vs. character-based methods. istance-based: Ultrametric Trees dditive Trees. haracter-based: Perfect phylogeny
More information进化树构建方法的概率方法 第 4 章 : 进化树构建的概率方法 问题介绍. 部分 lid 修改自 i i f l 的 ih l i
第 4 章 : 进化树构建的概率方法 问题介绍 进化树构建方法的概率方法 部分 lid 修改自 i i f l 的 ih l i 部分 Slides 修改自 University of Basel 的 Michael Springmann 课程 CS302 Seminar Life Science Informatics 的讲义 Phylogenetic Tree branch internal node
More informationBioinformatics tools for phylogeny and visualization. Yanbin Yin
Bioinformatics tools for phylogeny and visualization Yanbin Yin 1 Homework assignment 5 1. Take the MAFFT alignment http://cys.bios.niu.edu/yyin/teach/pbb/purdue.cellwall.list.lignin.f a.aln as input and
More informationMolecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals
Project Report Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals By Shubhra Gupta CBS 598 Phylogenetic Biology and Analysis Life Science
More informationLife in an unusual intracellular niche a bacterial symbiont infecting the nucleus of amoebae
Life in an unusual intracellular niche a bacterial symbiont infecting the nucleus of amoebae Frederik Schulz, Ilias Lagkouvardos, Florian Wascher, Karin Aistleitner, Rok Kostanjšek, Matthias Horn Supplementary
More informationUsing Bioinformatics to Study Evolutionary Relationships Instructions
3 Using Bioinformatics to Study Evolutionary Relationships Instructions Student Researcher Background: Making and Using Multiple Sequence Alignments One of the primary tasks of genetic researchers is comparing
More informationAssessing an Unknown Evolutionary Process: Effect of Increasing Site- Specific Knowledge Through Taxon Addition
Assessing an Unknown Evolutionary Process: Effect of Increasing Site- Specific Knowledge Through Taxon Addition David D. Pollock* and William J. Bruno* *Theoretical Biology and Biophysics, Los Alamos National
More informationPhylogenetic Trees. Phylogenetic Trees Five. Phylogeny: Inference Tool. Phylogeny Terminology. Picture of Last Quagga. Importance of Phylogeny 5.
Five Sami Khuri Department of Computer Science San José State University San José, California, USA sami.khuri@sjsu.edu v Distance Methods v Character Methods v Molecular Clock v UPGMA v Maximum Parsimony
More informationComparison and Analysis of Heat Shock Proteins in Organisms of the Kingdom Viridiplantae. Emily Germain, Rensselaer Polytechnic Institute
Comparison and Analysis of Heat Shock Proteins in Organisms of the Kingdom Viridiplantae Emily Germain, Rensselaer Polytechnic Institute Mentor: Dr. Hugh Nicholas, Biomedical Initiative, Pittsburgh Supercomputing
More informationLecture 4: Evolutionary models and substitution matrices (PAM and BLOSUM).
1 Bioinformatics: In-depth PROBABILITY & STATISTICS Spring Semester 2011 University of Zürich and ETH Zürich Lecture 4: Evolutionary models and substitution matrices (PAM and BLOSUM). Dr. Stefanie Muff
More information1. Can we use the CFN model for morphological traits?
1. Can we use the CFN model for morphological traits? 2. Can we use something like the GTR model for morphological traits? 3. Stochastic Dollo. 4. Continuous characters. Mk models k-state variants of the
More informationBioinformatics Exercises
Bioinformatics Exercises AP Biology Teachers Workshop Susan Cates, Ph.D. Evolution of Species Phylogenetic Trees show the relatedness of organisms Common Ancestor (Root of the tree) 1 Rooted vs. Unrooted
More informationEVOLUTIONARY DISTANCE MODEL BASED ON DIFFERENTIAL EQUATION AND MARKOV PROCESS
August 0 Vol 4 No 005-0 JATIT & LLS All rights reserved ISSN: 99-8645 wwwjatitorg E-ISSN: 87-95 EVOLUTIONAY DISTANCE MODEL BASED ON DIFFEENTIAL EUATION AND MAKOV OCESS XIAOFENG WANG College of Mathematical
More informationOutline. I. Methods. II. Preliminary Results. A. Phylogeny Methods B. Whole Genome Methods C. Horizontal Gene Transfer
Comparative Genomics Preliminary Results April 4, 2016 Juan Castro, Aroon Chande, Cheng Chen, Evan Clayton, Hector Espitia, Alli Gombolay, Walker Gussler, Ken Lee, Tyrone Lee, Hari Prasanna, Carlos Ruiz,
More informationdoi: / _25
Boc, A., P. Legendre and V. Makarenkov. 2013. An efficient algorithm for the detection and classification of horizontal gene transfer events and identification of mosaic genes. Pp. 253-260 in: B. Lausen,
More informationMapping QTL to a phylogenetic tree
Mapping QTL to a phylogenetic tree Karl W Broman Department of Biostatistics & Medical Informatics University of Wisconsin Madison www.biostat.wisc.edu/~kbroman Human vs mouse www.daviddeen.com 3 Intercross
More information