4.8 Article

Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains

Related references

Note: Only part of the references are listed.
Article Evolutionary Biology

Phylogenomics with incomplete taxon coverage: the limits to inference

Michael J. Sanderson et al.

BMC EVOLUTIONARY BIOLOGY (2010)

Article Evolutionary Biology

Evolution of the MAGUK protein gene family in premetazoan lineages

Alex de Mendoza et al.

BMC EVOLUTIONARY BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Compositional Heterogeneity and Phylogenomic Inference of Metazoan Relationships

Maximilian P. Nesnidal et al.

MOLECULAR BIOLOGY AND EVOLUTION (2010)

Article Biochemistry & Molecular Biology

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

K. S. Pick et al.

MOLECULAR BIOLOGY AND EVOLUTION (2010)

Article Multidisciplinary Sciences

Ancient origin of the integrin-mediated adhesion and signaling machinery

Arnau Sebe-Pedros et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Editorial Material Biochemistry & Molecular Biology

Evolution: Revisiting the Root of the Eukaryote Tree

Andrew J. Roger et al.

CURRENT BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Phylogeny of the Forgotten Cellular Slime Mold, Fonticula alba, Reveals a Key Evolutionary Branch within Opisthokonta

Matthew W. Brown et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Article Multidisciplinary Sciences

The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome-Wide EST Data

Jose Eduardo de la Torre-Barcena et al.

PLOS ONE (2009)

Article Multidisciplinary Sciences

The Evolutionary History of Protein Domains Viewed by Species Phylogeny

Song Yang et al.

PLOS ONE (2009)

Article Biology

Evolutionary position of breviate amoebae and the primary eukaryote divergence

Marianne A. Minge et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2009)

Article Biochemistry & Molecular Biology

Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern Urmetazoon Hypothesis

Bernd Schierwater et al.

PLOS BIOLOGY (2009)

Article Biochemical Research Methods

Model-based prediction of sequence alignment quality

Virpi Ahola et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

Sudhir Kumar et al.

BRIEFINGS IN BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

A phylogenomic investigation into the origin of metazoa

Inaki Ruiz-Trillo et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Biochemistry & Molecular Biology

A site- and time-heterogeneous model of amino acid replacement

Samuel Blanquart et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Biochemistry & Molecular Biology

An improved general amino acid replacement matrix

Si Quang Le et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Multidisciplinary Sciences

Multigene Phylogeny of Choanozoa and the Origin of Animals

Kamran Shalchian-Tabrizi et al.

PLOS ONE (2008)

Article Multidisciplinary Sciences

The Early ANTP Gene Repertoire: Insights from the Placozoan Genome

Bernd Schierwater et al.

PLOS ONE (2008)

Article Biology

Problematica old and new

Ronald A. Jenner et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2008)

Article Biology

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

Nicolas Lartillot et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2008)

Review Biotechnology & Applied Microbiology

Large-scale assignment of orthology: back to phylogenetics?

Toni Gabaldon

GENOME BIOLOGY (2008)

Article Biochemistry & Molecular Biology

Do we need many genes for phylogenetic inference?

V. V. Aleshin et al.

BIOCHEMISTRY-MOSCOW (2007)

Article Biochemical Research Methods

AxPcoords & parallel AxParafit:: statistical co-phylogenetic analyses on thousands of taxa

Alexandros Stamatakis et al.

BMC BIOINFORMATICS (2007)

Article Multidisciplinary Sciences

Phylogenomics Reshuffles the Eukaryotic Supergroups

Fabien Burki et al.

PLOS ONE (2007)

Article Evolutionary Biology

Detecting and overcoming systematic errors in genome-scale phylogenies

Naiara Rodriguez-Ezpeleta et al.

SYSTEMATIC BIOLOGY (2007)

Review Ecology

The supermatrix approach to systematics

Alan de Queiroz et al.

TRENDS IN ECOLOGY & EVOLUTION (2007)

Review Genetics & Heredity

The origins of multicellularity: a multi-taxon genome initiative

Inaki Ruiz-Trillo et al.

TRENDS IN GENETICS (2007)

Article Biochemistry & Molecular Biology

A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution

Samuel Blanquart et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Article Biochemical Research Methods

RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Alexandros Stamatakis

BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

AUGUSTUS:: ab initio prediction of alternative transcripts

Mario Stanke et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Multidisciplinary Sciences

Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum

SL Dellaporta et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Review Genetics & Heredity

Phylogenomics: the beginning of incongruence?

O Jeffroy et al.

TRENDS IN GENETICS (2006)

Article Biochemistry & Molecular Biology

The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic

JL Huang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Review Evolutionary Biology

An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics

H Brinkmann et al.

SYSTEMATIC BIOLOGY (2005)

Article Biochemistry & Molecular Biology

Biases in phylogenetic estimation can be caused by random sequence segments

E Susko et al.

JOURNAL OF MOLECULAR EVOLUTION (2005)

Review Genetics & Heredity

Phylogenomics and the reconstruction of the tree of life

F Delsuc et al.

NATURE REVIEWS GENETICS (2005)

Article Multidisciplinary Sciences

Phylogeny determined by protein domain content

S Yang et al.

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

Review Biochemistry & Molecular Biology

Phylogenomics of eukaryotes: Impact of missing data on large alignments

H Philippe et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Review Cell Biology

The unicellular ancestry of animal development

N King

DEVELOPMENTAL CELL (2004)

Letter Biochemistry & Molecular Biology

Capsaspora owczarzaki is an independent opisthokont lineage

I Ruiz-Trillo et al.

CURRENT BIOLOGY (2004)

Article Biochemistry & Molecular Biology

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

N Lartillot et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Evolutionary Biology

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood

S Guindon et al.

SYSTEMATIC BIOLOGY (2003)

Article Biochemistry & Molecular Biology

An evolutionarily structured universe of protein architecture

G Caetano-Anollés et al.

GENOME RESEARCH (2003)

Article Biochemistry & Molecular Biology

ExPASy: the proteomics server for in-depth protein knowledge and analysis

E Gasteiger et al.

NUCLEIC ACIDS RESEARCH (2003)

Review Biochemistry & Molecular Biology

Phylogeny of choanozoa, apusozoa, and other protozoa and early eukaryote megaevolution

T Cavalier-Smith et al.

JOURNAL OF MOLECULAR EVOLUTION (2003)

Article Biochemistry & Molecular Biology

Placozoa are not derived Cnidarians: Evidence from molecular morphology

A Ender et al.

MOLECULAR BIOLOGY AND EVOLUTION (2003)

Article Biochemistry & Molecular Biology

The closest unicellular relatives of animals

BF Lang et al.

CURRENT BIOLOGY (2002)

Article Biochemistry & Molecular Biology

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

K Katoh et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Evolutionary Biology

An approximately unbiased test of phylogenetic tree selection

H Shimodaira

SYSTEMATIC BIOLOGY (2002)

Article Biochemical Research Methods

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

HA Schmidt et al.

BIOINFORMATICS (2002)

Article Microbiology

The phagotrophic origin of eukaryotes and phylogenetic classification of protozoa

T Cavalier-Smith

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2002)

Article Evolutionary Biology

Inferring the root of a phylogenetic tree

JP Huelsenbeck et al.

SYSTEMATIC BIOLOGY (2002)

Article Biochemical Research Methods

CONSEL: for assessing the confidence of phylogenetic tree selection

H Shimodaira et al.

BIOINFORMATICS (2001)

Article Biochemistry & Molecular Biology

Computational inference of homologous gene structures in the human genome

RF Yeh et al.

GENOME RESEARCH (2001)

Article Biochemistry & Molecular Biology

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

S Whelan et al.

MOLECULAR BIOLOGY AND EVOLUTION (2001)

Article Biochemistry & Molecular Biology

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

J Castresana

MOLECULAR BIOLOGY AND EVOLUTION (2000)