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Ancestral Sequence Reconstruction

David A Liberles (ed.)

Published in print:
2007
Published Online:
September 2008
ISBN:
9780199299188
eISBN:
9780191714979
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199299188.001.0001
Subject:
Biology, Evolutionary Biology / Genetics

Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological ... More


Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences

Tal Pupko, Adi Doron-Faigenboim, David A. Liberles, and Gina M. Cannarozzi

in Ancestral Sequence Reconstruction

Published in print:
2007
Published Online:
September 2008
ISBN:
9780199299188
eISBN:
9780191714979
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199299188.003.0004
Subject:
Biology, Evolutionary Biology / Genetics

Modeling of sequence evolution is fundamental to ancestral sequence reconstruction. Care must be taken in choosing a model, however, as the use of unrealistic models can lead to erroneous ... More


The limits of conventional cladistic analysis

Jerrold I. Davis, Kevin C. Nixon, and Damon P. Little

in Parsimony, Phylogeny, and Genomics

Published in print:
2006
Published Online:
September 2007
ISBN:
9780199297306
eISBN:
9780191713729
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199297306.003.0007
Subject:
Biology, Evolutionary Biology / Genetics

Software for cladistic analysis has been widely available for more than twenty years, and a series of advances made during this time have facilitated the analysis of matrices of ever-increasing size. ... More


Using phylogeny to understand genomic evolution

David A. Liberles

in Parsimony, Phylogeny, and Genomics

Published in print:
2006
Published Online:
September 2007
ISBN:
9780199297306
eISBN:
9780191713729
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199297306.003.0010
Subject:
Biology, Evolutionary Biology / Genetics

As genome sequencing projects have propagated, comparative genomics has emerged as a method of choice for understanding protein function. There are simple approaches for comparing sequences, like ... More


Molecular Evolution: A Statistical Approach

Ziheng Yang

Published in print:
2014
Published Online:
August 2014
ISBN:
9780199602605
eISBN:
9780191782251
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199602605.001.0001
Subject:
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Evolutionary Biology / Genetics

This book summarizes the statistical models and computational algorithms for comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, and ... More


Phylogeny reconstruction: overview

ZIHENG YANG

in Computational Molecular Evolution

Published in print:
2006
Published Online:
April 2010
ISBN:
9780198567028
eISBN:
9780191728280
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198567028.003.0003
Subject:
Biology, Evolutionary Biology / Genetics

This chapter provides an overview of phylogeny reconstruction methods. It introduces some basic concepts used to describe trees and discusses general features of tree-reconstruction methods. Distance ... More


Comparison of methods and tests on trees

ZIHENG YANG

in Computational Molecular Evolution

Published in print:
2006
Published Online:
April 2010
ISBN:
9780198567028
eISBN:
9780191728280
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198567028.003.0006
Subject:
Biology, Evolutionary Biology / Genetics

This chapter discusses two problems: the evaluation of statistical properties of tree reconstruction methods and tests of the significance of estimated phylogenies. Section 6.1 discusses criteria for ... More


How Can We Reconstruct Evolutionary History?

Michel Laurin

in How Vertebrates Left the Water

Published in print:
2010
Published Online:
March 2012
ISBN:
9780520266476
eISBN:
9780520947986
Item type:
chapter
Publisher:
University of California Press
DOI:
10.1525/california/9780520266476.003.0001
Subject:
Biology, Evolutionary Biology / Genetics

This chapter attempts to reconstruct evolutionary history. Inferring phylogenetic relationships between taxa and character evolution requires relatively sophisticated methods. The chapter describes ... More


Phylogeny reconstruction: overview

Ziheng Yang

in Molecular Evolution: A Statistical Approach

Published in print:
2014
Published Online:
August 2014
ISBN:
9780199602605
eISBN:
9780191782251
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199602605.003.0003
Subject:
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Evolutionary Biology / Genetics

This chapter introduces basic concepts related to phylogenetic trees such as rooted and unrooted trees, consensus trees and partition distance, species trees, and gene trees. It discusses general ... More


Comparison of phylogenetic methods and tests on trees

Ziheng Yang

in Molecular Evolution: A Statistical Approach

Published in print:
2014
Published Online:
August 2014
ISBN:
9780199602605
eISBN:
9780191782251
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199602605.003.0005
Subject:
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Evolutionary Biology / Genetics

This chapter summarizes the criteria for comparing different tree reconstruction methods, such as consistency and efficiency, as well as computer simulation studies that evaluate the statistical ... More


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