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Phylogenetics PowerPoint PPT Presentation
Phylogenetics - Bat wing, human arm and cat front leg. Genes can also be homologous. 13. Morphological analysis ... Alopex (Arctic fox) Pseudoalopex (South American foxes) ...
Bat wing, human arm and cat front leg. Genes can also be homologous. 13. Morphological analysis ... Alopex (Arctic fox) Pseudoalopex (South American foxes) ...
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Phylogenetics%20I PowerPoint PPT Presentation
Phylogenetics%20I - White-fronted capuchin. Slow loris. Tree shrew. Japanese pipistrelle. Long-tailed bat ... White-fronted capuchin. Slow loris. Squirrel. Dormouse. Cane-rat ...
White-fronted capuchin. Slow loris. Tree shrew. Japanese pipistrelle. Long-tailed bat ... White-fronted capuchin. Slow loris. Squirrel. Dormouse. Cane-rat ...
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Phylogenetics PowerPoint PPT Presentation
Phylogenetics - Edges can be directed, then (vi,vj) is viewed as different ... Example: Human, Chimp, Gorilla & Orangutan with root. position 1 2 3 4 5 6 7 8 9 12.586 ...
Edges can be directed, then (vi,vj) is viewed as different ... Example: Human, Chimp, Gorilla & Orangutan with root. position 1 2 3 4 5 6 7 8 9 12.586 ...
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Molecular phylogenetics 1 PowerPoint PPT Presentation
Molecular phylogenetics 1 - Parsimony analysis identifies seven substitutions and places them on the five ... Under parsimony each site requires one change, which gives a total of seven changes ...
Parsimony analysis identifies seven substitutions and places them on the five ... Under parsimony each site requires one change, which gives a total of seven changes ...
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Phylogenetics II PowerPoint PPT Presentation
Phylogenetics II - One common approach is Maximum Parsimony. Common Assumptions: ... By the parsimony principle, we seek a tree that has a minimum total number of ...
One common approach is Maximum Parsimony. Common Assumptions: ... By the parsimony principle, we seek a tree that has a minimum total number of ...
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Molecular Phylogenetics PowerPoint PPT Presentation
Molecular Phylogenetics - Phenetic approach: Trees are based on some measure of distance between the leaves ... either cladistic (e.g. gene order) or phenetic ...
Phenetic approach: Trees are based on some measure of distance between the leaves ... either cladistic (e.g. gene order) or phenetic ...
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CS 177 Phylogenetics I PowerPoint PPT Presentation
CS 177 Phylogenetics I - Phylogenetic trees. Cladistic versus phenetic analyses. Model of sequence evolution ... Branch length (scaled trees only): represents the number of changes that have ...
Phylogenetic trees. Cladistic versus phenetic analyses. Model of sequence evolution ... Branch length (scaled trees only): represents the number of changes that have ...
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Statistical Phylogenetics PowerPoint PPT Presentation
Statistical Phylogenetics - ( Courtesy of NCBI Gen Bank) ... USA 103, 2845-2850. Fig. 1. Map of eastern Asia showing Fujian, Guangdong, Guangxi, Guizhou, Hong ...
( Courtesy of NCBI Gen Bank) ... USA 103, 2845-2850. Fig. 1. Map of eastern Asia showing Fujian, Guangdong, Guangxi, Guizhou, Hong ...
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Molecular phylogenetics 2 PowerPoint PPT Presentation
Molecular phylogenetics 2 - Distance methods are based on the idea that if we knew the evolutionary ... Gibbon. Orang-utan. 49. 34.5. 8.5. 44.5. 26. 94. 75. Algorithms for finding distance trees ...
Distance methods are based on the idea that if we knew the evolutionary ... Gibbon. Orang-utan. 49. 34.5. 8.5. 44.5. 26. 94. 75. Algorithms for finding distance trees ...
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Phylogenetics PowerPoint PPT Presentation
Phylogenetics - 'Thou art my brother but a few sequences removed' Generate topologies of evolutionary ... 'Its just a bruise, not Kaposi's sarcoma!' Maximum Likelihood ' ...
'Thou art my brother but a few sequences removed' Generate topologies of evolutionary ... 'Its just a bruise, not Kaposi's sarcoma!' Maximum Likelihood ' ...
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Molecular phylogenetics 3 PowerPoint PPT Presentation
Molecular phylogenetics 3 - Gibbon A C C G C C C C C A 0 0 0 0 0 0 0 0 0 0. 5 7 6 11 5 12 7 7 6 3. Spectral analysis ... In this case, the best non-trivial split is {Orang-utan, Gibbon} ...
Gibbon A C C G C C C C C A 0 0 0 0 0 0 0 0 0 0. 5 7 6 11 5 12 7 7 6 3. Spectral analysis ... In this case, the best non-trivial split is {Orang-utan, Gibbon} ...
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Molecular phylogenetics 4 PowerPoint PPT Presentation
Molecular phylogenetics 4 - In some cases (e.g. UPGMA) the phylogenetic method is simple enough that we can ... Rapid cladogenesis. Widely differing rates of divergence. Horizontal gene transfer ...
In some cases (e.g. UPGMA) the phylogenetic method is simple enough that we can ... Rapid cladogenesis. Widely differing rates of divergence. Horizontal gene transfer ...
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Plant Molecular Systematics (Phylogenetics) PowerPoint PPT Presentation
Plant Molecular Systematics (Phylogenetics) - Plant Molecular Systematics (Phylogenetics) Plant Molecular Systematics (Phylogenetics) BY: Mary Beth Craig Definitions Wikipedia.com defines Molecular Systematics ...
Plant Molecular Systematics (Phylogenetics) Plant Molecular Systematics (Phylogenetics) BY: Mary Beth Craig Definitions Wikipedia.com defines Molecular Systematics ...
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Challenges in computational phylogenetics PowerPoint PPT Presentation
Challenges in computational phylogenetics - Consensus/clustering methods for sets of optimal trees ... Because trees can change in biologically significant ways with small changes in ...
Consensus/clustering methods for sets of optimal trees ... Because trees can change in biologically significant ways with small changes in ...
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General Phylogenetics PowerPoint PPT Presentation
General Phylogenetics - (These will often be used to represent species or individual ... Wilson's General Rule: 60-80, is there other evidence to support the relationship, be cautious; ...
(These will often be used to represent species or individual ... Wilson's General Rule: 60-80, is there other evidence to support the relationship, be cautious; ...
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Introduction to phylogenetics PowerPoint PPT Presentation
Introduction to phylogenetics - Charles Darwin was the first to see clearly that evolutionary biology implies a tree like form ... Charles Darwin, On the Origin of Species; pages 131-132 ...
Charles Darwin was the first to see clearly that evolutionary biology implies a tree like form ... Charles Darwin, On the Origin of Species; pages 131-132 ...
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Phylogenetics and the Tree of Life PowerPoint PPT Presentation
Phylogenetics and the Tree of Life - Linnaeus originally divided all known forms of life between animal and plant ... Begins with binomial nomenclature. Progresses upwards, becoming more inclusive ...
Linnaeus originally divided all known forms of life between animal and plant ... Begins with binomial nomenclature. Progresses upwards, becoming more inclusive ...
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Johns Hopkins University - Fall 2003 Phylogenetics PowerPoint PPT Presentation
Johns Hopkins University - Fall 2003 Phylogenetics - d(AB)C / 2. B. C. step 1 step 2. UPGMA example. Lecture #6 Page 19 ... that other methods (e.g. minimum evolution) will evaluate to find the best tree. Exercises ...
d(AB)C / 2. B. C. step 1 step 2. UPGMA example. Lecture #6 Page 19 ... that other methods (e.g. minimum evolution) will evaluate to find the best tree. Exercises ...
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RNA functions, structure and Phylogenetics PowerPoint PPT Presentation
RNA functions, structure and Phylogenetics - RNA functions, structure and Phylogenetics * * * * * * * * * * * * * * * * RNA functions Storage/transfer of genetic information Genomes many viruses have RNA ...
RNA functions, structure and Phylogenetics * * * * * * * * * * * * * * * * RNA functions Storage/transfer of genetic information Genomes many viruses have RNA ...
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Computational and mathematical challenges involved in very large-scale phylogenetics PowerPoint PPT Presentation
Computational and mathematical challenges involved in very large-scale phylogenetics - Modelling variation between characters: Rates-across-sites ... Modelling variation between characters: The 'no-common-mechanism' model ...
Modelling variation between characters: Rates-across-sites ... Modelling variation between characters: The 'no-common-mechanism' model ...
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Advances and Limitations of Maximum Likelihood Phylogenetics PowerPoint PPT Presentation
Advances and Limitations of Maximum Likelihood Phylogenetics - The SPR procedure involves testing all (subtree, edge) pairs ... was estimated using XRATE (Holmes et al 06) EM-based software, with site likelihood ...
The SPR procedure involves testing all (subtree, edge) pairs ... was estimated using XRATE (Holmes et al 06) EM-based software, with site likelihood ...
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Biodiversity conservation using Phylogenetics on a global scale Klaas Hartmann TAFI, University of Tasmania PowerPoint PPT Presentation
Biodiversity conservation using Phylogenetics on a global scale Klaas Hartmann TAFI, University of Tasmania - Maximimizing phylogenetic diversity in biodiversity conservation: greedy ... Stochastic properties of generalised Yule models, with biodiversity applications. ...
Maximimizing phylogenetic diversity in biodiversity conservation: greedy ... Stochastic properties of generalised Yule models, with biodiversity applications. ...
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Phylogenetics Marek Kimmel Statistics, Rice kimmelrice'edu 713 348 5255 PowerPoint PPT Presentation
Phylogenetics Marek Kimmel Statistics, Rice kimmelrice'edu 713 348 5255 - ... by Maximum Likelihood (PAML) 3.0, University College London, London, England. ... Maps functionally important residues (FIR) onto surface. Trace Integral ...
... by Maximum Likelihood (PAML) 3.0, University College London, London, England. ... Maps functionally important residues (FIR) onto surface. Trace Integral ...
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Statistical Phylogenetics: An Application to Corbiculate Bees and Geography PowerPoint PPT Presentation
Statistical Phylogenetics: An Application to Corbiculate Bees and Geography - Investigate evolutionary relationships using similarity in ... Bombini: Bumble bee. Important for crop and wildflower pollination. Form small social colonies ...
Investigate evolutionary relationships using similarity in ... Bombini: Bumble bee. Important for crop and wildflower pollination. Form small social colonies ...
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APPLICABILITY OF SEQUENCE DIVERSITY AT MITOCHONDRIAL GENES ON DIFFERENT TAXONOMIC LEVELS IN GENETICS OF SPECIATION, PHYLOGENETICS AND BARCODING PowerPoint PPT Presentation
APPLICABILITY OF SEQUENCE DIVERSITY AT MITOCHONDRIAL GENES ON DIFFERENT TAXONOMIC LEVELS IN GENETICS OF SPECIATION, PHYLOGENETICS AND BARCODING - Halibut-like flatfish, Hypoglossus elasodon (A) and ... Plot of p-distance on number of splittings at Cyt-b sequence data for catfishes and flatfishes. ...
Halibut-like flatfish, Hypoglossus elasodon (A) and ... Plot of p-distance on number of splittings at Cyt-b sequence data for catfishes and flatfishes. ...
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Computational and mathematical challenges involved in very largescale phylogenetics PowerPoint PPT Presentation
Computational and mathematical challenges involved in very largescale phylogenetics - Performance of TNT with time. FN: false negative (missing edge) FP: false positive ... 'Perfect Phylogenetic Network' (all characters compatible) ...
Performance of TNT with time. FN: false negative (missing edge) FP: false positive ... 'Perfect Phylogenetic Network' (all characters compatible) ...
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Phylogenetics the science of identifying and understanding evolutionary relationship between differe PowerPoint PPT Presentation
Phylogenetics the science of identifying and understanding evolutionary relationship between differe - Sampling a set of species according to a given time ... determining the relationship among a set of species by appealing to an authoritative tree ...
Sampling a set of species according to a given time ... determining the relationship among a set of species by appealing to an authoritative tree ...
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Phylogeography PowerPoint PPT Presentation
Phylogeography - Phylogeography Phylogenetics Understanding phylogenetic trees Major approaches to determining phylogenies Phylogeography
Phylogeography Phylogenetics Understanding phylogenetic trees Major approaches to determining phylogenies Phylogeography
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Phylogenetic Analysis PowerPoint PPT Presentation
Phylogenetic Analysis - Phylogenetics Get related sequences of interest Perform multiple sequence alignments Edit alignment Estimate phylogenetic relationships Interpret results correctly ...
Phylogenetics Get related sequences of interest Perform multiple sequence alignments Edit alignment Estimate phylogenetic relationships Interpret results correctly ...
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*Less than 10% Dinosaur content PowerPoint PPT Presentation
*Less than 10% Dinosaur content - Methods covered: Sequence Alignment (& BLAST) Phylogenetics. Sequence Reconstruction. Sequence Alignment. How can we compare sequences? Simple scoring function. 1 for ...
Methods covered: Sequence Alignment (& BLAST) Phylogenetics. Sequence Reconstruction. Sequence Alignment. How can we compare sequences? Simple scoring function. 1 for ...
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Phylogenetic Analysis PowerPoint PPT Presentation
Phylogenetic Analysis - Phylogenetic Analysis General comments on phylogenetics Phylogenetics is the branch of biology that deals with evolutionary relatedness Uses some measure of ...
Phylogenetic Analysis General comments on phylogenetics Phylogenetics is the branch of biology that deals with evolutionary relatedness Uses some measure of ...
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http://creativecommons.org/licenses/by-sa/2.0/ PowerPoint PPT Presentation
http://creativecommons.org/licenses/by-sa/2.0/ - http://creativecommons.org/licenses/by-sa/2.0/ BNFO 602 Lecture 1 Usman Roshan Phylogenetics Study of how species relate to each other Nothing in biology makes ...
http://creativecommons.org/licenses/by-sa/2.0/ BNFO 602 Lecture 1 Usman Roshan Phylogenetics Study of how species relate to each other Nothing in biology makes ...
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Systematics and the Phylogenetic Revolution PowerPoint PPT Presentation
Systematics and the Phylogenetic Revolution - Cladistics - distinguishes ancestral from shared characters ... Cladistics ... Systematic phylogenetics is based on evolutionary relationships using cladistics. ...
Cladistics - distinguishes ancestral from shared characters ... Cladistics ... Systematic phylogenetics is based on evolutionary relationships using cladistics. ...
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Heron Island, GBR PowerPoint PPT Presentation
Heron Island, GBR - Heron Island, GBR. A Primer on Phylogenetics of Holothuroids. alexander.kerr@aya.yale.edu ... Best when rates of evolution are slow. Maximum parsimony. Maximum ...
Heron Island, GBR. A Primer on Phylogenetics of Holothuroids. alexander.kerr@aya.yale.edu ... Best when rates of evolution are slow. Maximum parsimony. Maximum ...
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Classification of Organisms PowerPoint PPT Presentation
Classification of Organisms - The goal is to classify organisms in terms of their natural relationships Phylogenetics The analysis of the evolutionary or ancestral relationships among taxa.
The goal is to classify organisms in terms of their natural relationships Phylogenetics The analysis of the evolutionary or ancestral relationships among taxa.
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Tree Reconstruction PowerPoint PPT Presentation
Tree Reconstruction - Basic Principles of Phylogenetics Distance Parsimony Compatibility Inconsistency Likelihood Tree Reconstruction * * * * * * Should be after stoch.proc. * * Find ...
Basic Principles of Phylogenetics Distance Parsimony Compatibility Inconsistency Likelihood Tree Reconstruction * * * * * * Should be after stoch.proc. * * Find ...
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GRAPPA: Large-scale whole genome phylogenies based upon gene order evolution PowerPoint PPT Presentation
GRAPPA: Large-scale whole genome phylogenies based upon gene order evolution - GRAPPA: Large-scale whole genome phylogenies based upon gene order evolution ... Center for Computational Biology and Bioinformatics. Whole-Genome Phylogenetics. A. B ...
GRAPPA: Large-scale whole genome phylogenies based upon gene order evolution ... Center for Computational Biology and Bioinformatics. Whole-Genome Phylogenetics. A. B ...
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Introduction to Computational Biology PowerPoint PPT Presentation
Introduction to Computational Biology - Kimura's two-parameter model. Molecular clock. Relative rate test. Phylogenetics ... Quantile normalization. Quality control. Data distributions. Histograms. boxplots ...
Kimura's two-parameter model. Molecular clock. Relative rate test. Phylogenetics ... Quantile normalization. Quality control. Data distributions. Histograms. boxplots ...
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Dan Graur PowerPoint PPT Presentation
Dan Graur - Molecular Phylogenetics Dan Graur * * Maximize the probability of observing the data of aligned sequences conditional on a particular tree structure by trying all ...
Molecular Phylogenetics Dan Graur * * Maximize the probability of observing the data of aligned sequences conditional on a particular tree structure by trying all ...
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Assessing reliability of results measures of clade support PowerPoint PPT Presentation
Assessing reliability of results measures of clade support - Likelihood only: Parametric bootstrap (simulation of data) ... Likelihood-Based Tests of Topologies in Phylogenetics. Systematic Biology 49, (652-670) ...
Likelihood only: Parametric bootstrap (simulation of data) ... Likelihood-Based Tests of Topologies in Phylogenetics. Systematic Biology 49, (652-670) ...
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BB10B Introductory Microbiology PowerPoint PPT Presentation
BB10B Introductory Microbiology - Phylogenetics, tree of life, nomenclature. Lecture 2 Friday 20th Feb 9am. Metabolic diversity ... The tree of life. Eukaryote, prokaryote what is the difference? ...
Phylogenetics, tree of life, nomenclature. Lecture 2 Friday 20th Feb 9am. Metabolic diversity ... The tree of life. Eukaryote, prokaryote what is the difference? ...
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Grids : from life sciences to healthcare PowerPoint PPT Presentation
Grids : from life sciences to healthcare - ... the infrastructure to deploy biomedical applications in a grid ... status of biomedical applications. Bio-informatics. Phylogenetics : BBE Lyon (T. Sylvestre) ...
... the infrastructure to deploy biomedical applications in a grid ... status of biomedical applications. Bio-informatics. Phylogenetics : BBE Lyon (T. Sylvestre) ...
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Dan Graur PowerPoint PPT Presentation
Dan Graur - In molecular phylogenetics: A clade is a group of taxa under study that share a common ancestor, which is not shared by any other species outside the group.
In molecular phylogenetics: A clade is a group of taxa under study that share a common ancestor, which is not shared by any other species outside the group.
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New Tools for Visualizing Genome Evolution PowerPoint PPT Presentation
New Tools for Visualizing Genome Evolution - Our research focuses on how information can be gained from the molecular record: ... using phylogenetics will be a key ingredient to unravel the life's early history. ...
Our research focuses on how information can be gained from the molecular record: ... using phylogenetics will be a key ingredient to unravel the life's early history. ...
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What if anything is a burrowing pika PowerPoint PPT Presentation
What if anything is a burrowing pika - Life history traits of pikas. Smith 1988: Evolution of life histories of mammals, Smith et al. ... Pika evolution. Yu et al. 2000, Molecular Phylogenetics and ...
Life history traits of pikas. Smith 1988: Evolution of life histories of mammals, Smith et al. ... Pika evolution. Yu et al. 2000, Molecular Phylogenetics and ...
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Darwin 1856 PowerPoint PPT Presentation
Darwin 1856 - Phylogenetic systematics (Cladistics) Hennig (1960s-1970s) DNA sequences (1970s) ... THE SIMPLIFIED HISTORY OF SYSTEMATICS -Hillis, et al, 1996 ...
Phylogenetic systematics (Cladistics) Hennig (1960s-1970s) DNA sequences (1970s) ... THE SIMPLIFIED HISTORY OF SYSTEMATICS -Hillis, et al, 1996 ...
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Phylogenetic%20Analysis PowerPoint PPT Presentation
Phylogenetic%20Analysis - What is phylogenetic analysis and why should we perform it? Phylogenetic analysis has two major components: (1) Phylogeny inference or tree building
What is phylogenetic analysis and why should we perform it? Phylogenetic analysis has two major components: (1) Phylogeny inference or tree building
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Phylogenetic methods PowerPoint PPT Presentation
Phylogenetic methods - Darwin using Linnaeus's classification hierarchy ... 0.33% sequences difference among ethic groups (5% between orangutan subspecies) ...
Darwin using Linnaeus's classification hierarchy ... 0.33% sequences difference among ethic groups (5% between orangutan subspecies) ...
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MODELS OF PROTEIN EVOLUTION: AN INTRODUCTION TO AMINO ACID EXCHANGE MATRICES PowerPoint PPT Presentation
MODELS OF PROTEIN EVOLUTION: AN INTRODUCTION TO AMINO ACID EXCHANGE MATRICES - LS. ME. NJ. Distance calculation (which model?) Model? MP. Wheighting? ... Construction of phylogenetic trees. Science 155, 279-284. Phylogenies from proteins ...
LS. ME. NJ. Distance calculation (which model?) Model? MP. Wheighting? ... Construction of phylogenetic trees. Science 155, 279-284. Phylogenies from proteins ...
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Phylogenetic Analysis and Classification PowerPoint PPT Presentation
Phylogenetic Analysis and Classification - Contrary to phenetic approaches, phylogenetic algorithms retain individuality of ... Wiley, E. O., D. Siegel-Causey, D. R. Brooks, and V. A. Funk. 1991. ...
Contrary to phenetic approaches, phylogenetic algorithms retain individuality of ... Wiley, E. O., D. Siegel-Causey, D. R. Brooks, and V. A. Funk. 1991. ...
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Bioinformatics PowerPoint PPT Presentation
Bioinformatics - Bioinformatics GUEST LECTURE : Phylogenetic Trees Ronald Westra, Biomathematics Group, Maastricht University
Bioinformatics GUEST LECTURE : Phylogenetic Trees Ronald Westra, Biomathematics Group, Maastricht University
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IE68 Biological databases Phylogenetic analysis PowerPoint PPT Presentation
IE68 Biological databases Phylogenetic analysis - a reconstruction of the evolutionary (genealogical) history of a group of ... e.g. forensic science. IE68 - biological databases - phylogeny ...
a reconstruction of the evolutionary (genealogical) history of a group of ... e.g. forensic science. IE68 - biological databases - phylogeny ...
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Phylogenetic study of Aedes albopictus and Aedes koreicus (Diptera, Culicidae) origin, two invasive mosquito species in Belgium PowerPoint PPT Presentation
Phylogenetic study of Aedes albopictus and Aedes koreicus (Diptera, Culicidae) origin, two invasive mosquito species in Belgium - Discovery of these two invasive species suggests a ... Coosemans M, Van Bortel W: Bionomics of the established exotic mosquito species Aedes koreicus in Belgium, Europe.
Discovery of these two invasive species suggests a ... Coosemans M, Van Bortel W: Bionomics of the established exotic mosquito species Aedes koreicus in Belgium, Europe.
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Phylogenetic Tree Reconstruction PowerPoint PPT Presentation
Phylogenetic Tree Reconstruction - Define a node k with daughter nodes i and j, and place it at. height di,j/2. ... dAC dBD= dAD dBC= a b c d 2x = dAB dCD 2x. The 4-point condition ...
Define a node k with daughter nodes i and j, and place it at. height di,j/2. ... dAC dBD= dAD dBC= a b c d 2x = dAB dCD 2x. The 4-point condition ...
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