Presentation is loading. Please wait.

Presentation is loading. Please wait.

Distance based phylogeny reconstruction

Published byDorothée Sénéchal Modified over 6 years ago

Similar presentations

Presentation on theme: "Distance based phylogeny reconstruction"— Presentation transcript:

1 Distance based phylogeny reconstruction
Usman Roshan

2 Distance-based methods

3 Evolutionary distances for aligned sequences
We will use the Jukes Cantor model x and y are DNA/protein/RNA sequences p(x,y) is the number of mismatches in the alignment divided by the length of the alignment. This is also called the normalized Hamming distance.

4 Evolutionary distances for whole genomes
A kmer is a substring of length k We will use an approximation to Jukes Cantor x and y are whole genome sequences This method does not require sequences to be aligned.

Download ppt "Distance based phylogeny reconstruction"

Similar presentations

1 Orthologs: Two genes, each from a different species, that descended from a single common ancestral gene Paralogs: Two or more genes, often thought of.

1 Orthologs: Two genes, each from a different species, that descended from a single common ancestral gene Paralogs: Two or more genes, often thought of.
$100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300.

$100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300.
Bayesian Evolutionary Distance P. Agarwal and D.J. States. Bayesian evolutionary distance. Journal of Computational Biology 3(1):1— 17, 1996.

Bayesian Evolutionary Distance P. Agarwal and D.J. States. Bayesian evolutionary distance. Journal of Computational Biology 3(1):1— 17, 1996.
Phylogenetic trees Sushmita Roy BMI/CS 576 Sep 23 rd, 2014.

Phylogenetic trees Sushmita Roy BMI/CS 576 Sep 23 rd, 2014.
Introduction BNFO 602 Usman Roshan. Course grade Project: –Find a bioinformatics topic by Feb 5th. This can be a paper or a research question you wish.

Introduction BNFO 602 Usman Roshan. Course grade Project: –Find a bioinformatics topic by Feb 5th. This can be a paper or a research question you wish.
On the complexity of finding common approximate substrings Theoretical Computer Science 306 (2003) 407-430 Patricia A. Evans, Andrew D. Smith, H. Todd.

On the complexity of finding common approximate substrings Theoretical Computer Science 306 (2003) Patricia A. Evans, Andrew D. Smith, H. Todd.
CIS786, Lecture 7 Usman Roshan Some of the slides are based upon material by Dennis Livesay and David.

CIS786, Lecture 7 Usman Roshan Some of the slides are based upon material by Dennis Livesay and David.
BME 130 – Genomes Lecture 26 Molecular phylogenies I.

BME 130 – Genomes Lecture 26 Molecular phylogenies I.
Hidden Markov Models Usman Roshan BNFO 601. Hidden Markov Models Alphabet of symbols: Set of states that emit symbols from the alphabet: Set of probabilities.

Hidden Markov Models Usman Roshan BNFO 601. Hidden Markov Models Alphabet of symbols: Set of states that emit symbols from the alphabet: Set of probabilities.
Pairwise profile alignment Usman Roshan BNFO 601.

Pairwise profile alignment Usman Roshan BNFO 601.
CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Distance Matrix Methods: Models of Evolution Anders Gorm Pedersen Molecular Evolution Group Center for Biological.

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Distance Matrix Methods: Models of Evolution Anders Gorm Pedersen Molecular Evolution Group Center for Biological.
BNFO 602 Multiple sequence alignment Usman Roshan.

BNFO 602 Multiple sequence alignment Usman Roshan.
BNFO 235 Lecture 5 Usman Roshan. What we have done to date Basic Perl –Data types: numbers, strings, arrays, and hashes –Control structures: If-else,

BNFO 235 Lecture 5 Usman Roshan. What we have done to date Basic Perl –Data types: numbers, strings, arrays, and hashes –Control structures: If-else,
BNFO 602 Phylogenetics Usman Roshan. Summary of last time Models of evolution Distance based tree reconstruction –Neighbor joining –UPGMA.

BNFO 602 Phylogenetics Usman Roshan. Summary of last time Models of evolution Distance based tree reconstruction –Neighbor joining –UPGMA.
CIS786, Lecture 8 Usman Roshan Some of the slides are based upon material by Dennis Livesay and David.

CIS786, Lecture 8 Usman Roshan Some of the slides are based upon material by Dennis Livesay and David.
Phylogenetic trees Sushmita Roy BMI/CS 576

Phylogenetic trees Sushmita Roy BMI/CS 576
$100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300.

$100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300 $400 $500 $100 $200 $300.
Whole genome comparison Kelley Crouse And Greg Matuszek.

Whole genome comparison Kelley Crouse And Greg Matuszek.
Phylogenetic Reconstruction based on RNA Secondary Structural Alignment Benny Chor, Tel-Aviv Univ. Joint work with Moran Cabili, Assaf Meirovich, and Metsada.

Phylogenetic Reconstruction based on RNA Secondary Structural Alignment Benny Chor, Tel-Aviv Univ. Joint work with Moran Cabili, Assaf Meirovich, and Metsada.
Bioinformatics 2011 Molecular Evolution Revised 29/12/06.

Bioinformatics 2011 Molecular Evolution Revised 29/12/06.

Similar presentations

Ads by Google