4.7 Article

The impact of HGT on phylogenomic reconstruction methods

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Microbiology

Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades

Hafiz Sohail Naushad et al.

ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2012)

Article Biology

Biased gene transfer and its implications for the concept of lineage

Cheryl P. Andam et al.

BIOLOGY DIRECT (2011)

Review Biology

A Rooted Net of Life

David Williams et al.

BIOLOGY DIRECT (2011)

Article Evolutionary Biology

Evaluating Phylogenetic Congruence in the Post-Genomic Era

Jessica W. Leigh et al.

GENOME BIOLOGY AND EVOLUTION (2011)

Article Biochemistry & Molecular Biology

Quantifying Nonvertical Inheritance in the Evolution of Legionella pneumophila

Mireia Coscolla et al.

MOLECULAR BIOLOGY AND EVOLUTION (2011)

Review Microbiology

Biased gene transfer in microbial evolution

Cheryl P. Andam et al.

NATURE REVIEWS MICROBIOLOGY (2011)

Article Biochemical Research Methods

A simulation study comparing supertree and combined analysis methods using SMIDGen

M. Shel Swenson et al.

ALGORITHMS FOR MOLECULAR BIOLOGY (2010)

Article Biochemical Research Methods

Robinson-Foulds Supertrees

Mukul S. Bansal et al.

ALGORITHMS FOR MOLECULAR BIOLOGY (2010)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Review Biology

Prokaryotic evolution and the tree of life are two different things

Eric Bapteste et al.

BIOLOGY DIRECT (2009)

Article Genetics & Heredity

A likelihood look at the supermatrix-supertree controversy

Fengrong Ren et al.

Article Evolutionary Biology

Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus

Olga Zhaxybayeva et al.

GENOME BIOLOGY AND EVOLUTION (2009)

Article Multidisciplinary Sciences

On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales

Olga Zhaxybayeva et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Genetics & Heredity

Estimating the size of the bacterial pan-genome

Pascal Lapierrel et al.

TRENDS IN GENETICS (2009)

Article Evolutionary Biology

Testing congruence in phylogenomic analysis

Jessica W. Leigh et al.

SYSTEMATIC BIOLOGY (2008)

Article Biochemistry & Molecular Biology

PAML 4: Phylogenetic analysis by maximum likelihood

Ziheng Yang

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Evolutionary Biology

Profiling phylogenetic informativeness

Jeffrey P. Townsend

SYSTEMATIC BIOLOGY (2007)

Article Biochemical Research Methods

A simulation test bed for hypotheses of genome evolution

Robert G. Beiko et al.

BIOINFORMATICS (2007)

Article Multidisciplinary Sciences

Pattern pluralism and the Tree of Life hypothesis

W. Ford Doolittle et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Evolutionary Biology

Inconsistency of phylogenetic estimates from concatenated data under coalescence

Laura Salter Kubatko et al.

SYSTEMATIC BIOLOGY (2007)

Article Evolutionary Biology

Imputing supertrees and supernetworks from quartets

B. Holland et al.

SYSTEMATIC BIOLOGY (2007)

Review Ecology

The supermatrix approach to systematics

Alan de Queiroz et al.

TRENDS IN ECOLOGY & EVOLUTION (2007)

Article Biochemistry & Molecular Biology

Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events

Olga Zhaxybayeva et al.

GENOME RESEARCH (2006)

Article Genetics & Heredity

Discordance of species trees with their most likely gene trees

James H. Degnan et al.

PLOS GENETICS (2006)

Review Genetics & Heredity

Phylogenomics: the beginning of incongruence?

O Jeffroy et al.

TRENDS IN GENETICS (2006)

Article Multidisciplinary Sciences

Toward automatic reconstruction of a highly resolved tree of life

FD Ciccarelli et al.

SCIENCE (2006)

Article Evolutionary Biology

SDM: A fast distance-based approach for (super) tree building in phylogenomics

Alexis Criscuolo et al.

SYSTEMATIC BIOLOGY (2006)

Article Biochemical Research Methods

Use of artificial genomes in assessing methods for atypical gene detection

RK Azad et al.

PLOS COMPUTATIONAL BIOLOGY (2005)

Article Multidisciplinary Sciences

Highways of gene sharing in prokaryotes

RG Beiko et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae:: Implications for the microbial pan-genome

H Tettelin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Microbiology

Towards a genome-based taxonomy for prokaryotes

KT Konstantinidis et al.

JOURNAL OF BACTERIOLOGY (2005)

Article Biochemistry & Molecular Biology

The net of life: Reconstructing the microbial phylogenetic network

V Kunin et al.

GENOME RESEARCH (2005)

Article Evolutionary Biology

The shape of supertrees to come: Tree shape related properties of fourteen supertree methods

M Wilkinson et al.

SYSTEMATIC BIOLOGY (2005)

Article Biochemical Research Methods

Clann: investigating phylogenetic information through supertree analyses

CJ Creevey et al.

BIOINFORMATICS (2005)

Review Microbiology

Horizontal gene transfer, genome innovation and evolution

JP Gogarten et al.

NATURE REVIEWS MICROBIOLOGY (2005)

Review Ecology

The evolution of supertrees

ORP Bininda-Emonds

TRENDS IN ECOLOGY & EVOLUTION (2004)

Article Microbiology

Caloramator viterbensis sp nov., a novel thermophilic, glycerol-fermenting bacterium isolated from a hot spring in Italy

M Seyfried et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2002)

Article Mathematics, Applied

Geometry of the space of phylogenetic trees

LJ Billera et al.

ADVANCES IN APPLIED MATHEMATICS (2001)

Letter Genetics & Heredity

Universal trees based on large combined protein sequence data sets

JR Brown et al.

NATURE GENETICS (2001)

Review Multidisciplinary Sciences

Lateral gene transfer and the nature of bacterial innovation

H Ochman et al.

NATURE (2000)

Article Multidisciplinary Sciences

Uprooting the tree of life

WF Doolittle

SCIENTIFIC AMERICAN (2000)