Symmetric Tree, ClustalW. Divergence x 0.5 Divergence x 1 Divergence x 2. Alignment length
|
|
|
- Basil Poole
- 5 years ago
- Views:
Transcription
1 ONLINE APPENDIX Talavera, G., and Castresana, J. (). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, -. Symmetric Tree, ClustalW Divergence x. Divergence x Divergence x ClustalW, Gblocks relaxed ClustalW, Gblocks stringent Online Appendix - Figure. Average Robinson-Foulds distances to the real from the calculated with ClustalW alignments (solid, red line), and the same alignments after treatment with Gblocks relaxed (dotted, blue line with diamonds) and stringent (dotted, green line with square symbols) conditions. The symmetric with three different divergence levels was used for the simulations. Trees were reconstructed by ML, NJ and parsimony.
2 Intermediate Tree, ClustalW Divergence x. Divergence x Divergence x ClustalW, Gblocks relaxed ClustalW, Gblocks stringent Online Appendix - Figure. Average Robinson-Foulds distances to the real from the calculated with ClustalW alignments (solid, red line), and the same alignments after treatment with Gblocks relaxed (dotted, blue line with diamonds) and stringent (dotted, green line with square symbols) conditions. The intermediate with three different divergence levels was used for the simulations. Not all alignment lengths were simulated. Trees were reconstructed by ML, NJ and parsimony.
3 Symmetric Tree, Mafft Divergence x. Divergence x Divergence x Online Appendix - Figure. Average Robinson-Foulds distances to the real from the calculated with Mafft alignments (solid, red line), and the same alignments after treatment with Gblocks relaxed (dotted, blue line with diamonds) and stringent (dotted, green line with square symbols) conditions. The symmetric with three different divergence levels was used for the simulations. Trees were reconstructed by ML, NJ and parsimony.
4 Intermediate Tree, Mafft Divergence x. Divergence x Divergence x Online Appendix - Figure. Average Robinson-Foulds distances to the real from the calculated with Mafft alignments (solid, red line), and the same alignments after treatment with Gblocks relaxed (dotted, blue line with diamonds) and stringent (dotted, green line with square symbols) conditions. The intermediate with three different divergence levels was used for the simulations. Not all alignment lengths were simulated. Trees were reconstructed by ML, NJ and parsimony.
5 KOG Divergence x. Divergence x Divergence x KOG Online Appendix - Figure. Average Robinson-Foulds distances to the real from the ML calculated with Mafft complete alignments (solid, red line), and the same alignments after treatment with Gblocks relaxed (dotted, blue line with diamonds) and stringent (dotted, green line with squared symbols) conditions. The asymmetric with three different divergence levels was used for the simulations. Profiles of rate heterogeneity derived from two different proteins, KOG and KOG, were used.
6 amino acids amino acids Asymmetric Intermediate Symmetric Asymmetric Intermediate Symmetric ML Divergence x. Divergence x Divergence x NJ Divergence x. Divergence x Divergence x Divergence x. Divergence x Divergence x ClustalW, GBlocks relaxed ClustalW, GBlocks stringent Mafft, GBlocks relaxed Mafft, GBlocks stringent Online Appendix - Figure. Overall alignment strategies that give rise to the statistically best topologies. The complete alignment is represented by a black rectangle (ClustalW) or oval (Mafft), and the two different Gblocks strategies by rectangles or ovals with stripes that represent the stringency of the selection.
7 Bootstrap analysis Symmetric Tree - NJ A 9 Divergence x. Divergence x Divergence x ClustalW, Gblocks relaxed ClustalW, Gblocks stringent B 9 Online Appendix - Figure. Average bootstrap values of NJ s obtained from ClustalW (A) and Mafft (B) alignments simulated from the symmetric with three different divergence levels. Complete (solid, red line), Gblocks relaxed (dotted, blue line with diamonds) and Gblocks stringent (dotted, green line with squared symbols) alignments are shown.
8 Bootstrap analysis Asymmetric Tree - ML A 9 Divergence x. Divergence x Divergence x ClustalW, Gblocks relaxed ClustalW, Gblocks stringent B 9 Online Appendix - Figure. Average bootstrap values of ML s obtained from ClustalW (A) and Mafft (B) alignments simulated from the asymmetric with three different divergence levels. Complete (solid, red line), Gblocks relaxed (dotted, blue line with diamonds) and Gblocks stringent (dotted, green line with squared symbols) alignments are shown.
Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
Syst. Biol. 56(4)564-577, 2007 Copyright Society of Systematic Biologists ISSN: 1063-5157 print / 1076-836X online DOI: 10.1080/10635150701472164 Improvement of Phylogenies after Removing Divergent and
Elements of Bioinformatics 14F01 TP5 -Phylogenetic analysis
Elements of Bioinformatics 14F01 TP5 -Phylogenetic analysis 10 December 2012 - Corrections - Exercise 1 Non-vertebrate chordates generally possess 2 homologs, vertebrates 3 or more gene copies; a Drosophila
Phylogenetics. Applications of phylogenetics. Unrooted networks vs. rooted trees. Outline
Phylogenetics Todd Vision iology 522 March 26, 2007 pplications of phylogenetics Studying organismal or biogeographic history Systematics ating events in the fossil record onservation biology Studying
Constructing 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
Amira 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
Phylogenetics: 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
Dr. 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
Phylogenetics: 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
Bioinformatics 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
Constructing 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
Phylogenetic inference
Phylogenetic inference Bas E. Dutilh Systems Biology: Bioinformatic Data Analysis Utrecht University, March 7 th 016 After this lecture, you can discuss (dis-) advantages of different information types
Introduction to Bioinformatics Introduction to Bioinformatics
Dr. rer. nat. Gong Jing Cancer Research Center Medicine School of Shandong University 2012.11.09 1 Chapter 4 Phylogenetic Tree 2 Phylogeny Evidence from morphological ( 形态学的 ), biochemical, and gene sequence
Inferring 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
Phylogenetic relationship among S. castellii, S. cerevisiae and C. glabrata.
Supplementary Note S2 Phylogenetic relationship among S. castellii, S. cerevisiae and C. glabrata. Phylogenetic trees reconstructed by a variety of methods from either single-copy orthologous loci (Class
POPULATION 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
InDel 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
A (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
C.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
NJMerge: 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
C3020 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
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11510 Supplementary Table 1. Indel Index Removal Gene Number of Starting Sequences Number of Final Sequences Percentage of Sequences Removed based on the Indel
Smith et al. American Journal of Botany 98(3): Data Supplement S2 page 1
Smith et al. American Journal of Botany 98(3):404-414. 2011. Data Supplement S1 page 1 Smith, Stephen A., Jeremy M. Beaulieu, Alexandros Stamatakis, and Michael J. Donoghue. 2011. Understanding angiosperm
A 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
Today's project. Test input data Six alignments (from six independent markers) of Curcuma species
DNA sequences II Analyses of multiple sequence data datasets, incongruence tests, gene trees vs. species tree reconstruction, networks, detection of hybrid species DNA sequences II Test of congruence of
A 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
Mul$ple Sequence Alignment Methods. Tandy Warnow Departments of Bioengineering and Computer Science h?p://tandy.cs.illinois.edu
Mul$ple Sequence Alignment Methods Tandy Warnow Departments of Bioengineering and Computer Science h?p://tandy.cs.illinois.edu Species Tree Orangutan Gorilla Chimpanzee Human From the Tree of the Life
Phylogenetic 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
MOLECULAR 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
Effects of Gap Open and Gap Extension Penalties
Brigham Young University BYU ScholarsArchive All Faculty Publications 200-10-01 Effects of Gap Open and Gap Extension Penalties Hyrum Carroll hyrumcarroll@gmail.com Mark J. Clement clement@cs.byu.edu See
Introduction to Bioinformatics Online Course: IBT
Introduction to Bioinformatics Online Course: IBT Multiple Sequence Alignment Building Multiple Sequence Alignment Lec1 Building a Multiple Sequence Alignment Learning Outcomes 1- Understanding Why multiple
Additive distances. w(e), where P ij is the path in T from i to j. Then the matrix [D ij ] is said to be additive.
![Additive distances. w(e), where P ij is the path in T from i to j. Then the matrix [D ij ] is said to be additive.](/thumbs/92/110439366.jpg "Additive distances. w(e), where P ij is the path in T from i to j. Then the matrix [D ij ] is said to be additive.")
Additive distances Let T be a tree on leaf set S and let w : E R + be an edge-weighting of T, and assume T has no nodes of degree two. Let D ij = e P ij w(e), where P ij is the path in T from i to j. Then
TheDisk-Covering MethodforTree Reconstruction
TheDisk-Covering MethodforTree Reconstruction Daniel Huson PACM, Princeton University Bonn, 1998 1 Copyright (c) 2008 Daniel Huson. Permission is granted to copy, distribute and/or modify this document
USE OF CLUSTERING TECHNIQUES FOR PROTEIN DOMAIN ANALYSIS
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Computer Science and Engineering: Theses, Dissertations, and Student Research Computer Science and Engineering, Department
SCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION. Using Anatomy, Embryology, Biochemistry, and Paleontology
SCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION Using Anatomy, Embryology, Biochemistry, and Paleontology Scientific Fields Different fields of science have contributed evidence for the theory of
Phylogenetic Tree Estimation With and Without Alignment: New Distance Methods and Benchmarking
Syst. Biol. 0(0):1 14, 2016 The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com
The 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
Phylogenies Scores for Exhaustive Maximum Likelihood and Parsimony Scores Searches
Int. J. Bioinformatics Research and Applications, Vol. x, No. x, xxxx Phylogenies Scores for Exhaustive Maximum Likelihood and s Searches Hyrum D. Carroll, Perry G. Ridge, Mark J. Clement, Quinn O. Snell
Phylogenetic 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,
"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2009 University of California, Berkeley
"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2009 University of California, Berkeley B.D. Mishler Jan. 22, 2009. Trees I. Summary of previous lecture: Hennigian
Some Problems from Enzyme Families
Some Problems from Enzyme Families Greg Butler Department of Computer Science Concordia University, Montreal www.cs.concordia.ca/~faculty/gregb gregb@cs.concordia.ca Abstract I will discuss some problems
Tree 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
Letter to the Editor. Department of Biology, Arizona State University
Letter to the Editor Traditional Phylogenetic Reconstruction Methods Reconstruct Shallow and Deep Evolutionary Relationships Equally Well Michael S. Rosenberg and Sudhir Kumar Department of Biology, Arizona
Session 5: Phylogenomics
Session 5: Phylogenomics B.- Phylogeny based orthology assignment REMINDER: Gene tree reconstruction is divided in three steps: homology search, multiple sequence alignment and model selection plus tree
DNA 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 :
Weighted Quartets Phylogenetics
Weighted Quartets Phylogenetics Yunan Luo E. Avni, R. Cohen, and S. Snir. Weighted quartets phylogenetics. Systematic Biology, 2014. syu087 Problem: quartet-based supertree Input Output A B C D A C D E
Phylogenetics: 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
Maximum Likelihood Tree Estimation. Carrie Tribble IB Feb 2018
Maximum Likelihood Tree Estimation Carrie Tribble IB 200 9 Feb 2018 Outline 1. Tree building process under maximum likelihood 2. Key differences between maximum likelihood and parsimony 3. Some fancy extras
Thanks to Paul Lewis, Jeff Thorne, and Joe Felsenstein for the use of slides
hanks to Paul Lewis, Jeff horne, and Joe Felsenstein for the use of slides Hennigian logic reconstructs the tree if we know polarity of characters and there is no homoplasy UPM infers a tree from a distance
Department of Computer Science, Technical University of Munich, Bolzmannstr. 3, 85747, Garching b. Mu nchen, Germany 2
Phylogenetic Bootstrapping under Resource Constraints: Higher Model Accuracy or more Replicates? Alexandros Stamatakis 1* and Vincent Rousset 2 1 Department of Computer Science, Technical University of
Lecture 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
"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
A Method of Alignment Masking for Refining the Phylogenetic Signal of Multiple Sequence Alignments
Article: Methods A Method of Alignment Masking for Refining the Phylogenetic Signal of Multiple Sequence Alignments Vaibhav Rajan* Research Scientist, Xerox Research Centre India, Bangalore, India *This
Biology 559R: Introduction to Phylogenetic Comparative Methods Topics for this week (Jan 27 & 29):
Biology 559R: Introduction to Phylogenetic Comparative Methods Topics for this week (Jan 27 & 29): Statistical estimation of models of sequence evolution Phylogenetic inference using maximum likelihood:
Bootstrapping and Tree reliability. Biol4230 Tues, March 13, 2018 Bill Pearson Pinn 6-057
Bootstrapping and Tree reliability Biol4230 Tues, March 13, 2018 Bill Pearson wrp@virginia.edu 4-2818 Pinn 6-057 Rooting trees (outgroups) Bootstrapping given a set of sequences sample positions randomly,
Algorithmic 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
This course is taught completely online through UF e-learning; no scheduled meeting times
MCB 4934 / 6937 Special Topics Molecular Bioinformatics in UNIX 3 credits This course is taught completely online through UF e-learning; no scheduled meeting times Prerequisites Undergraduate: MCB 3020
The Phylogenetic Reconstruction of the Grass Family (Poaceae) Using matk Gene Sequences
The Phylogenetic Reconstruction of the Grass Family (Poaceae) Using matk Gene Sequences by Hongping Liang Dissertation submitted to the Faculty of the Virginia Polytechnic Institute and State University
Biology 2. Lecture Material. For. Macroevolution. Systematics
Biology 2 Macroevolution & Systematics 1 Biology 2 Lecture Material For Macroevolution & Systematics Biology 2 Macroevolution & Systematics 2 Microevolution: Biological Species: Two Patterns of Evolutionary
Bioinformatics 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
RESEARCH ARTICLES. Mayo Roettger, William Martin, and Tal Dagan
RESEARCH ARTICLES A Machine-Learning Approach Reveals That Alignment Properties Alone Can Accurately Predict Inference of Lateral Gene Transfer from Discordant Phylogenies Mayo Roettger, William Martin,
7. 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
Phylogeny of Mixture Models
Phylogeny of Mixture Models Daniel Štefankovič Department of Computer Science University of Rochester joint work with Eric Vigoda College of Computing Georgia Institute of Technology Outline Introduction
PhyQuart-A new algorithm to avoid systematic bias & phylogenetic incongruence
PhyQuart-A new algorithm to avoid systematic bias & phylogenetic incongruence Are directed quartets the key for more reliable supertrees? Patrick Kück Department of Life Science, Vertebrates Division,
林仲彥. Dec 4,
林仲彥 cylin@iis.sinica.edu.tw Dec 4, 2009 http://eln.iis.sinica.edu.tw Coding Characters and Defining Homology Classical phylogenetic analysis by Morphology Molecular phylogenetic analysis By Bio-Molecules
Molecular 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
Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley
Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley B.D. Mishler Feb. 14, 2018. Phylogenetic trees VI: Dating in the 21st century: clocks, & calibrations;
Consistency Index (CI)
Consistency Index (CI) minimum number of changes divided by the number required on the tree. CI=1 if there is no homoplasy negatively correlated with the number of species sampled Retention Index (RI)
CHAPTERS 24-25: Evidence for Evolution and Phylogeny
CHAPTERS 24-25: Evidence for Evolution and Phylogeny 1. For each of the following, indicate how it is used as evidence of evolution by natural selection or shown as an evolutionary trend: a. Paleontology
Likelihood Ratio Tests for Detecting Positive Selection and Application to Primate Lysozyme Evolution
Likelihood Ratio Tests for Detecting Positive Selection and Application to Primate Lysozyme Evolution Ziheng Yang Department of Biology, University College, London An excess of nonsynonymous substitutions
Supplemental Data. Perea-Resa et al. Plant Cell. (2012) /tpc
Supplemental Data. Perea-Resa et al. Plant Cell. (22)..5/tpc.2.3697 Sm Sm2 Supplemental Figure. Sequence alignment of Arabidopsis LSM proteins. Alignment of the eleven Arabidopsis LSM proteins. Sm and
From Phylogenetics to Phylogenomics: The Evolutionary Relationships of Insect Endosymbiotic γ-proteobacteria as a Test Case
Syst. Biol. 56(1):1 16, 2007 Copyright c Society of Systematic Biologists ISSN: 1063-5157 print / 1076-836X online DOI: 10.1080/10635150601109759 From Phylogenetics to Phylogenomics: The Evolutionary Relationships
Phylogenetic 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
08/21/2017 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
Theory of Evolution Charles Darwin
Theory of Evolution Charles arwin 858-59: Origin of Species 5 year voyage of H.M.S. eagle (83-36) Populations have variations. Natural Selection & Survival of the fittest: nature selects best adapted varieties
CONCEPT OF SEQUENCE COMPARISON. Natapol Pornputtapong 18 January 2018
CONCEPT OF SEQUENCE COMPARISON Natapol Pornputtapong 18 January 2018 SEQUENCE ANALYSIS - A ROSETTA STONE OF LIFE Sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of
Theory of Evolution. Charles Darwin
Theory of Evolution harles arwin 858-59: Origin of Species 5 year voyage of H.M.S. eagle (8-6) Populations have variations. Natural Selection & Survival of the fittest: nature selects best adapted varieties
Assessing 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
Comparison of Cost Functions in Sequence Alignment. Ryan Healey
Comparison of Cost Functions in Sequence Alignment Ryan Healey Use of Cost Functions Used to score and align sequences Mathematically model how sequences mutate and evolve. Evolution and mutation can be
THEORY. 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
Molecular phylogeny How to infer phylogenetic trees using molecular sequences
Molecular phylogeny How to infer phylogenetic trees using molecular sequences ore Samuelsson Nov 2009 Applications of phylogenetic methods Reconstruction of evolutionary history / Resolving taxonomy issues
Molecular phylogeny How to infer phylogenetic trees using molecular sequences
Molecular phylogeny How to infer phylogenetic trees using molecular sequences ore Samuelsson Nov 200 Applications of phylogenetic methods Reconstruction of evolutionary history / Resolving taxonomy issues
Reconstruire le passé biologique modèles, méthodes, performances, limites
Reconstruire le passé biologique modèles, méthodes, performances, limites Olivier Gascuel Centre de Bioinformatique, Biostatistique et Biologie Intégrative C3BI USR 3756 Institut Pasteur & CNRS Reconstruire
Anatomy 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
Algorithms in Bioinformatics
Algorithms in Bioinformatics Sami Khuri Department of Computer Science San José State University San José, California, USA khuri@cs.sjsu.edu www.cs.sjsu.edu/faculty/khuri Distance Methods Character Methods
Phylogene)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:
Phylogenetic Tree Reconstruction
I519 Introduction to Bioinformatics, 2011 Phylogenetic Tree Reconstruction Yuzhen Ye (yye@indiana.edu) School of Informatics & Computing, IUB Evolution theory Speciation Evolution of new organisms is driven
Why IQ-TREE? Bui Quang Minh Australian National University. Workshop on Molecular Evolution Woods Hole, 24 July 2018
Why IQ-R? ui Quang Minh ustralian National University Workshop on Molecular volution Woods Hole, 24 July 2018 hanks to plenty of users for feedback and bug reports! ypical phylogenetic analysis under maximum
Basics 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
Appendix A: Significant Figures and Error Analysis
1 Appendix A: Significant Figures and Error Analysis Every measurement of a physical quantity contains some amount of uncertainty or error. We often speak of a certain number or measurement as being precise
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
Published online 30 April 2010 W7 W13 doi:10.1093/nar/gkq291 TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations Federico Abascal 1, Rafael Zardoya 1 and Maximilian
Evolutionary Approaches to Sequence Alignment
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1723 Evolutionary Approaches to Sequence Alignment MARCIN BOGUSZ ACTA UNIVERSITATIS UPSALIENSIS UPPSALA
How to use CAOS software for taxonomy? quick guide to extract diagnostic nucleotides or amino acids for species descriptions.
SPIXIANA 37 1 21-26 München, August 2014 ISSN 0341-8391 How to use CAOS software for taxonomy? A quick guide to extract diagnostic nucleotides or amino acids for species descriptions Katharina M. Jörger
GENETICS - CLUTCH CH.22 EVOLUTIONARY GENETICS.
!! www.clutchprep.com CONCEPT: OVERVIEW OF EVOLUTION Evolution is a process through which variation in individuals makes it more likely for them to survive and reproduce There are principles to the theory
Improving divergence time estimation in phylogenetics: more taxa vs. longer sequences
Mathematical Statistics Stockholm University Improving divergence time estimation in phylogenetics: more taxa vs. longer sequences Bodil Svennblad Tom Britton Research Report 2007:2 ISSN 650-0377 Postal
9/30/11. Evolution theory. Phylogenetic Tree Reconstruction. Phylogenetic trees (binary trees) Phylogeny (phylogenetic tree)
I9 Introduction to Bioinformatics, 0 Phylogenetic ree Reconstruction Yuzhen Ye (yye@indiana.edu) School of Informatics & omputing, IUB Evolution theory Speciation Evolution of new organisms is driven by
MOLECULAR SYSTEMATICS: A SYNTHESIS OF THE COMMON METHODS AND THE STATE OF KNOWLEDGE
CELLULAR & MOLECULAR BIOLOGY LETTERS http://www.cmbl.org.pl Received: 16 August 2009 Volume 15 (2010) pp 311-341 Final form accepted: 01 March 2010 DOI: 10.2478/s11658-010-0010-8 Published online: 19 March
Maximum Likelihood Estimation on Large Phylogenies and Analysis of Adaptive Evolution in Human Influenza Virus A
J Mol Evol (2000) 51:423 432 DOI: 10.1007/s002390010105 Springer-Verlag New York Inc. 2000 Maximum Likelihood Estimation on Large Phylogenies and Analysis of Adaptive Evolution in Human Influenza Virus
arxiv: v1 [q-bio.pe] 1 Jun 2014
![arxiv: v1 [q-bio.pe] 1 Jun 2014](/thumbs/90/101381538.jpg "arxiv: v1 [q-bio.pe] 1 Jun 2014")
THE MOST PARSIMONIOUS TREE FOR RANDOM DATA MAREIKE FISCHER, MICHELLE GALLA, LINA HERBST AND MIKE STEEL arxiv:46.27v [q-bio.pe] Jun 24 Abstract. Applying a method to reconstruct a phylogenetic tree from
Phylogeny: 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
Systematics - Bio 615
Bayesian Phylogenetic Inference 1. Introduction, history 2. Advantages over ML 3. Bayes Rule 4. The Priors 5. Marginal vs Joint estimation 6. MCMC Derek S. Sikes University of Alaska 7. Posteriors vs Bootstrap