tree
... • Can only work for pairs of sequences that are similar enough to be aligned • All base changes are considered equal • Insertion/deletions are generally given a larger weight than replacements (gap penalties). • Possible to correct for multiple substitutions at a single site, which is common in dist ...
... • Can only work for pairs of sequences that are similar enough to be aligned • All base changes are considered equal • Insertion/deletions are generally given a larger weight than replacements (gap penalties). • Possible to correct for multiple substitutions at a single site, which is common in dist ...
3000_2013_1e
... • when and how were complex eyes evolved? in what species are they lost? are the genes required to develop eyes still there? can they be expressed in different ways? ...
... • when and how were complex eyes evolved? in what species are they lost? are the genes required to develop eyes still there? can they be expressed in different ways? ...
Chapter 20 Questions
... Suppose that species 1 and species 3 have similar appearances but very divergent gene sequences. Species 2 and species 3 have very different appearances but similar gene sequences. Which pair of species is more likely to be closely related: 1 and 2, or 2 and 3? Explain. ...
... Suppose that species 1 and species 3 have similar appearances but very divergent gene sequences. Species 2 and species 3 have very different appearances but similar gene sequences. Which pair of species is more likely to be closely related: 1 and 2, or 2 and 3? Explain. ...
Step 3. Construction of the phylogenetic tree Distance methods
... P = the fraction of sequence positions differing by a transition Q = the fraction of sequence positions differing by a transversion. ...
... P = the fraction of sequence positions differing by a transition Q = the fraction of sequence positions differing by a transversion. ...
Phylogenetic - Nematode bioinformatics. Analysis tools and data
... divergence order of taxa, as well as the lengths of the branches that connect them. There are many phylogenetic methods available today, each having strengths and weaknesses. Most can be classified as follows: ...
... divergence order of taxa, as well as the lengths of the branches that connect them. There are many phylogenetic methods available today, each having strengths and weaknesses. Most can be classified as follows: ...
m12-comparative_genomics
... the one that explains observed changes using the smallest number of point mutations o Maximum Likelihood: Analog of Maximum Parsimony that attempts to identify the most likely tree rather than the cheapest one; these are the most common methods used today A single-gene tree does not always reflect ...
... the one that explains observed changes using the smallest number of point mutations o Maximum Likelihood: Analog of Maximum Parsimony that attempts to identify the most likely tree rather than the cheapest one; these are the most common methods used today A single-gene tree does not always reflect ...
Creating Phylogenetic Trees with MEGA
... Kumar, S., Dudley, J., Nei, M., and Tamura, K., MEGA: A biologist‐centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299‐306 (2008) Hulsenbeck, J.P., and Ronquist, F., MyBayes: Bayesian inferences of phylogeny. Bioinformatics ...
... Kumar, S., Dudley, J., Nei, M., and Tamura, K., MEGA: A biologist‐centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299‐306 (2008) Hulsenbeck, J.P., and Ronquist, F., MyBayes: Bayesian inferences of phylogeny. Bioinformatics ...
Introduction to Phylogenetics - Lectures For UG-5
... Making trees using character-based methods The main idea of character based methods is to search for a tree that requires the smallest number of evolutionary changes to explain the differences among the OTUs under study. ...
... Making trees using character-based methods The main idea of character based methods is to search for a tree that requires the smallest number of evolutionary changes to explain the differences among the OTUs under study. ...
Diapositiva 1
... GENE PHYLOGENIES • Parsimony (Fitch 1977), • Pairwise distances (Saitou and Nei 1987), • Maximum likelihood (Felsenstein 1981): Use of explicit models of sequence evolution (computationally very intensive) Divergence dates of genes and species can also be estimated from phylogenetic distances (Ramb ...
... GENE PHYLOGENIES • Parsimony (Fitch 1977), • Pairwise distances (Saitou and Nei 1987), • Maximum likelihood (Felsenstein 1981): Use of explicit models of sequence evolution (computationally very intensive) Divergence dates of genes and species can also be estimated from phylogenetic distances (Ramb ...
Day6
... time, this process may repeat itself, so that at any time, each population can be said to be most closelyrelated to some other population with which it shares a direct common ancestor. ...
... time, this process may repeat itself, so that at any time, each population can be said to be most closelyrelated to some other population with which it shares a direct common ancestor. ...
Lecture5
... Creates noise in the data Some characters give conflicting information about relationships Systematists try to minimize homoplasy in a data set Choose characters that evolve slowly relative to age of taxa ...
... Creates noise in the data Some characters give conflicting information about relationships Systematists try to minimize homoplasy in a data set Choose characters that evolve slowly relative to age of taxa ...
Using HIV Data Sets for Inquiry
... • Minimizes distance between nearest neighbors Maximum parsimony • Minimizes total evolutionary change Maximum likelihood • Maximizes likelihood of observed data ...
... • Minimizes distance between nearest neighbors Maximum parsimony • Minimizes total evolutionary change Maximum likelihood • Maximizes likelihood of observed data ...
Comparative Anatomy: Phylogenetics Assignment
... 4. Print out a distance matrix in which you include all characters in the calculations. From looking at the distances, answer the following questions: a. Is there any reason to think that the dataset you are using will not be useful in determining phylogenetic relationships among taxa? Write your an ...
... 4. Print out a distance matrix in which you include all characters in the calculations. From looking at the distances, answer the following questions: a. Is there any reason to think that the dataset you are using will not be useful in determining phylogenetic relationships among taxa? Write your an ...
Slajd 1
... The construction of phylogenetic trees from numerical methods The principle of maximum parsimony (Occam’s razor) holds that we should accept that phylogenetic tree that can be constructed with the least number of morphological changes. The raw data Species A B C D E ...
... The construction of phylogenetic trees from numerical methods The principle of maximum parsimony (Occam’s razor) holds that we should accept that phylogenetic tree that can be constructed with the least number of morphological changes. The raw data Species A B C D E ...
CIPRES.2006.algorthms_sr
... • Breakthrough: Optimal logarithmic sequence length tree reconstruction (Daskalakis, Mossel, Roch 05). Simplified version (Mihaescu et al. 06). Preliminary Implementation [Adkins et al.]. ...
... • Breakthrough: Optimal logarithmic sequence length tree reconstruction (Daskalakis, Mossel, Roch 05). Simplified version (Mihaescu et al. 06). Preliminary Implementation [Adkins et al.]. ...
Diagrams Nov 8
... Phenetic: classification of the organisms based on their similarities, trees obtained using a phenetic approach may not reflect evolutionary relationships. A tree based on this method is called a phenogram Cladistic (Hennig 1966): study of the different pathways of evolution, the most parsimonious p ...
... Phenetic: classification of the organisms based on their similarities, trees obtained using a phenetic approach may not reflect evolutionary relationships. A tree based on this method is called a phenogram Cladistic (Hennig 1966): study of the different pathways of evolution, the most parsimonious p ...
Classification and phylogeny – Chapter 2
... (Cercopithecidae) and Homo – Oldest fossils of Cercopithidae are dated at 25 mya • Average rate for Rhesus monkey lineage = 457/25 my = 1.83 x 10-3 per my • Average rate for Homo line is 310/25 my = 1.24 x 10-3 per my • Average rate is 1.54 x 10-3 per my ...
... (Cercopithecidae) and Homo – Oldest fossils of Cercopithidae are dated at 25 mya • Average rate for Rhesus monkey lineage = 457/25 my = 1.83 x 10-3 per my • Average rate for Homo line is 310/25 my = 1.24 x 10-3 per my • Average rate is 1.54 x 10-3 per my ...
Trees
... Amino-acid sites are partially ordered characters. An amino acid cannot change into all other amino acids in a singe step, as sometimes 2 or 3 steps are required. For example, a tyrosine may only change into a leucine through an intermediate state, i.e., phenylalanine or histidine. ...
... Amino-acid sites are partially ordered characters. An amino acid cannot change into all other amino acids in a singe step, as sometimes 2 or 3 steps are required. For example, a tyrosine may only change into a leucine through an intermediate state, i.e., phenylalanine or histidine. ...
Phylogeny of the Primates
... As promised, you are going to get your chance to create a phylogenetic tree from some molecular clock data. We are going to give you some mutation differences in DNA. This is just like the bird phylogeny we did. Below is a table of REAL data. This date represents difference in DNA. It is obtained by ...
... As promised, you are going to get your chance to create a phylogenetic tree from some molecular clock data. We are going to give you some mutation differences in DNA. This is just like the bird phylogeny we did. Below is a table of REAL data. This date represents difference in DNA. It is obtained by ...
Phylogenetics Molecular Phylogenetics
... a problem because of some change in behaviour? Or is there another explanation for their origin? Host species tree ...
... a problem because of some change in behaviour? Or is there another explanation for their origin? Host species tree ...
Evolution, 2e
... Genes for 11 tRNAs 6 proteins Human-chimpanzee relationship 1023 more likely than Chimpanzee-gorilla relationship ...
... Genes for 11 tRNAs 6 proteins Human-chimpanzee relationship 1023 more likely than Chimpanzee-gorilla relationship ...
An Introduction to Phylogenetics
... more taxa that are known to have diverged prior to the group being studied • The node where the outgroup lineage joins the other taxa is the root ...
... more taxa that are known to have diverged prior to the group being studied • The node where the outgroup lineage joins the other taxa is the root ...
Lecture 7-POSTED-BISC441-2012
... for finding trees with the best value for the objective function. Can identify many equally optimal trees, if such exist. Warning: Finding an optimal tree is not necessarily the same as finding the "true” tree. Random data will give you an ‘optimal’ (best ) tree! ...
... for finding trees with the best value for the objective function. Can identify many equally optimal trees, if such exist. Warning: Finding an optimal tree is not necessarily the same as finding the "true” tree. Random data will give you an ‘optimal’ (best ) tree! ...
lecture 03 - phylogenetics - Cal State LA
... - how were ancestral traits modified in different lineages? A hypothesis of the evolutionary history of a group is called its phylogeny - often summarized in a branching diagram called a phylogenetic tree Since we can’t travel back in time to identify common ancestors, relationships of existing spec ...
... - how were ancestral traits modified in different lineages? A hypothesis of the evolutionary history of a group is called its phylogeny - often summarized in a branching diagram called a phylogenetic tree Since we can’t travel back in time to identify common ancestors, relationships of existing spec ...
