Different phylogenomic approaches to resolve the evolutionary relationships among model fish species (Q38444057)

3 September 2017

Different phylogenomic approaches to resolve the evolutionary relationships among model fish species (English)

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3 September 2017

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2

Heiner Kuhl

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3 September 2017

Enrico Negrisolo

1

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3 September 2017

Claudio Forcato

3

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3 September 2017

Nicola Vitulo

4

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3 September 2017

Richard Reinhardt

5

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3 September 2017

Tomaso Patarnello

6

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3 September 2017

Luca Bargelloni

7

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3 September 2017

29 June 2010

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Molecular Biology and Evolution

3 September 2017

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3 September 2017

27

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3 September 2017

12

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3 September 2017

2757-2774

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ProtTest: selection of best-fit models of protein evolution

3 September 2017

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

JIGSAW: integration of multiple sources of evidence for gene prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Basic local alignment search tool

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

A kingdom-level phylogeny of eukaryotes based on combined protein data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

21 January 2018

GeneWise and Genomewise

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Molecular phylogeny and divergence times of deuterostome animals

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Fast statistical alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Prediction of complete gene structures in human genomic DNA

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

DNA reference alignment benchmarks based on tertiary structure of encoded proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Novel evolutionary relationship among four fish model systems.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Fugu ESTs: new resources for transcription analysis and genome annotation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Mauve: multiple alignment of conserved genomic sequence with rearrangements

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Tunicates and not cephalochordates are the closest living relatives of vertebrates

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Broad phylogenomic sampling improves resolution of the animal tree of life

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Cases in which Parsimony or Compatibility Methods will be Positively Misleading

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Confidence Limits on Phylogenies: an Approach using the Bootstrap

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Molecular phylogeny of the animal kingdom

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

FusionDB: a database for in-depth analysis of prokaryotic gene fusion events

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Estimating maximum likelihood phylogenies with PhyML.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Benchmarking ortholog identification methods using functional genomics data

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Phylogenomics: the beginning of incongruence?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

RETRACTED: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

The medaka draft genome and insights into vertebrate genome evolution

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

MAFFT version 5: improvement in accuracy of multiple sequence alignment

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Determining the relative rates of change for prokaryotic and eukaryotic proteins with anciently duplicated paralogs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

The closest BLAST hit is often not the nearest neighbor.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Multiple sequence alignment: in pursuit of homologous DNA positions

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Versatile and open software for comparing large genomes

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

The quest for orthologs: finding the corresponding gene across genomes

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Selectionism and neutralism in molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Rooting the eutherian tree: the power and pitfalls of phylogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

The accuracy of several multiple sequence alignment programs for proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Large-scale sequencing and the new animal phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Genome-scale phylogeny and the detection of systematic biases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

MODELTEST: testing the model of DNA substitution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Genome-scale approaches to resolving incongruence in molecular phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

MrBayes 3: Bayesian phylogenetic inference under mixed models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Incomplete taxon sampling is not a problem for phylogenetic inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Taxon sampling, bioinformatics, and phylogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Acoel Flatworms: Earliest Extant Bilaterian Metazoans, Not Members of Platyhelminthes

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

A phylogenomic investigation into the origin of metazoa.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

An approximately unbiased test of phylogenetic tree selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Polyphyly of the mail-cheeked fishes (Teleostei: Scorpaeniformes): evidence from mitochondrial and nuclear sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Genome duplication, a trait shared by 22000 species of ray-finned fish

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Construction and characterization of a BAC library for the European sea bass Dicentrarchus labrax.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

An enhanced RNA alignment benchmark for sequence alignment programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Alignment uncertainty and genomic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

DAMBE: software package for data analysis in molecular biology and evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ165

21 January 2018

Identifiers

DOI

10.1093/MOLBEV/MSQ165

1 reference

3 September 2017

1 reference