m12-comparative_genomics

... Organize a collection of modern-day sequences according to their evolutionary history Distance-based methods operate on a table of pairwise distances between sequences o UPGMA: ~agglomerative clustering; naïve method for tree-building; assumes a molecular clock (all branches changing at the same ...

... Organize a collection of modern-day sequences according to their evolutionary history Distance-based methods operate on a table of pairwise distances between sequences o UPGMA: ~agglomerative clustering; naïve method for tree-building; assumes a molecular clock (all branches changing at the same ...

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. ...

Introduction to Phylogenetics - Lectures For UG-5

... Distance: the other type of data are distance data, which are computed from DNA or amino acid sequence data . These data are also called the distance matrix data, because the distance are usually presented in the matrix from. ...

... Distance: the other type of data are distance data, which are computed from DNA or amino acid sequence data . These data are also called the distance matrix data, because the distance are usually presented in the matrix from. ...

Phylogenetic - Nematode bioinformatics. Analysis tools and data

... Are mathematical and/or statistical methods for inferring the 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: Characters (bp, aa) Distance ...

... Are mathematical and/or statistical methods for inferring the 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: Characters (bp, aa) Distance ...

Diapositiva 1

... Distance trees were constructed using Neighbor-Joining with a maximum likelihood distance matrix using the model selected by MODELTEST. The standard errors of branch lengths were estimated using PAUP . Divergence dates with low and high confidence intervals and associated evolutionary rates were est ...

... Distance trees were constructed using Neighbor-Joining with a maximum likelihood distance matrix using the model selected by MODELTEST. The standard errors of branch lengths were estimated using PAUP . Divergence dates with low and high confidence intervals and associated evolutionary rates were est ...

Creating Phylogenetic Trees with MEGA

... – At each site, the likelihood is determined by evaluating the probability that a certain evolutionary model (eg. BLOSSUM or PAM matrices) has generated the observed data. – The likelihood’s for each site are then multiplied to provide likelihood for each tree – Choose the tree with maximum like ...

... – At each site, the likelihood is determined by evaluating the probability that a certain evolutionary model (eg. BLOSSUM or PAM matrices) has generated the observed data. – The likelihood’s for each site are then multiplied to provide likelihood for each tree – Choose the tree with maximum like ...

Day6

... • Phylogenetic analysis is one of the most controversial areas in bioinformatics. There are a wide variety of different methods for analyzing the data, and even the experts often disagree on the best method for analyzing the data. ...

... • Phylogenetic analysis is one of the most controversial areas in bioinformatics. There are a wide variety of different methods for analyzing the data, and even the experts often disagree on the best method for analyzing the data. ...

Phylogenetics Molecular Phylogenetics

... means that it lacks the common ancestor of (A) the species in the group. Furthermore, a valid taxon that includes the extant species G, H, J, and K would necessarily also contain D and E, which are also descended from A. ...

... means that it lacks the common ancestor of (A) the species in the group. Furthermore, a valid taxon that includes the extant species G, H, J, and K would necessarily also contain D and E, which are also descended from A. ...

Concept Check Questions

... Phylogenetic systematic informs the construction of phylogenetic trees based on shared characteristics ...

... Phylogenetic systematic informs the construction of phylogenetic trees based on shared characteristics ...

CSCE590/822 Data Mining Principles and Applications

... Assumptions fail when Highly dependent on evolution is rapid assumed evolution model ...

... Assumptions fail when Highly dependent on evolution is rapid assumed evolution model ...

An Introduction to Phylogenetics

... All of these representations depict the same topology Branch lengths are indicated in blue Red lengths are meaningless ...

... All of these representations depict the same topology Branch lengths are indicated in blue Red lengths are meaningless ...

Phylogenetic tree estimation

... Synteny & collinearity • Synteny gene loci are on the same chromosome ...

... Synteny & collinearity • Synteny gene loci are on the same chromosome ...

Step 3. Construction of the phylogenetic tree Distance methods

... Therefore, methods have been developed to compensate for this. ...

... Therefore, methods have been developed to compensate for this. ...

A method for paralogy trees reconstruction

... Genes belonging to the same organism are called paralogs when they show a significant similarity in the sequences, even if they have a different biological function. It is an emergent biological paradigm that the families of paralogs derive from a mechanism of gene duplication with modification, rep ...

... Genes belonging to the same organism are called paralogs when they show a significant similarity in the sequences, even if they have a different biological function. It is an emergent biological paradigm that the families of paralogs derive from a mechanism of gene duplication with modification, rep ...

Slides of Barbara`s talk - School of Mathematical Sciences

... *More generally, this could be a set of Q matrices ...

... *More generally, this could be a set of Q matrices ...