Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
出版年份 2019 全文链接
标题
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
作者
关键词
-
出版物
Nature Communications
Volume 10, Issue 1, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2019-12-02
DOI
10.1038/s41467-019-13443-4
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses
- (2019) Yuanqiang Zou et al. NATURE BIOTECHNOLOGY
- ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization
- (2019) John Yin et al. BIOINFORMATICS
- Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
- (2019) Evan Bolyen et al. NATURE BIOTECHNOLOGY
- ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
- (2018) Chao Zhang et al. BMC BIOINFORMATICS
- TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees
- (2018) Uyen Mai et al. BMC GENOMICS
- Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life
- (2018) Cindy J. Castelle et al. CELL
- DiscoVista: Interpretable visualizations of gene tree discordance
- (2018) Erfan Sayyari et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
- (2018) Andrew Rambaut et al. SYSTEMATIC BIOLOGY
- A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
- (2018) Donovan H Parks et al. NATURE BIOTECHNOLOGY
- Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction
- (2017) Erfan Sayyari et al. MOLECULAR BIOLOGY AND EVOLUTION
- UFBoot2: Improving the Ultrafast Bootstrap Approximation
- (2017) Diep Thi Hoang et al. MOLECULAR BIOLOGY AND EVOLUTION
- Asgard archaea illuminate the origin of eukaryotic cellular complexity
- (2017) Katarzyna Zaremba-Niedzwiedzka et al. NATURE
- Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
- (2017) Robert M Bowers et al. NATURE BIOTECHNOLOGY
- ModelFinder: fast model selection for accurate phylogenetic estimates
- (2017) Subha Kalyaanamoorthy et al. NATURE METHODS
- Archaea and the origin of eukaryotes
- (2017) Laura Eme et al. NATURE REVIEWS MICROBIOLOGY
- RefSeq: an update on prokaryotic genome annotation and curation
- (2017) Daniel H Haft et al. NUCLEIC ACIDS RESEARCH
- Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation
- (2017) Huai-Chun Wang et al. SYSTEMATIC BIOLOGY
- Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
- (2016) Erfan Sayyari et al. MOLECULAR BIOLOGY AND EVOLUTION
- Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
- (2016) Ivica Letunic et al. NUCLEIC ACIDS RESEARCH
- A new view of the tree of life
- (2016) Laura A. Hug et al. Nature Microbiology
- Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer
- (2015) Ruth Davidson et al. BMC GENOMICS
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences
- (2015) Siavash Mirarab et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Unusual biology across a group comprising more than 15% of domain Bacteria
- (2015) Christopher T. Brown et al. NATURE
- Rooting the tree of life: the phylogenetic jury is still out
- (2015) Richard Gouy et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Fast Dating Using Least-Squares Criteria and Algorithms
- (2015) Thu-Hien To et al. SYSTEMATIC BIOLOGY
- Ultra-large alignments using phylogeny-aware profiles
- (2015) Nam-phuong D. Nguyen et al. GENOME BIOLOGY
- Quality scores for 32,000 genomes
- (2015) Miriam L Land et al. Standards in Genomic Sciences
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
- (2014) Lam-Tung Nguyen et al. MOLECULAR BIOLOGY AND EVOLUTION
- Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?
- (2014) Hemalatha Golaconda Ramulu et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
- (2014) H Bjørn Nielsen et al. NATURE BIOTECHNOLOGY
- PhyloSift: phylogenetic analysis of genomes and metagenomes
- (2014) Aaron E. Darling et al. PeerJ
- Recovering the Treelike Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis
- (2013) Sebastien Roch et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
- (2013) K. Katoh et al. MOLECULAR BIOLOGY AND EVOLUTION
- Insights into the phylogeny and coding potential of microbial dark matter
- (2013) Christian Rinke et al. NATURE
- An archaeal origin of eukaryotes supports only two primary domains of life
- (2013) Tom A. Williams et al. NATURE
- UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota
- (2013) J. H. Campbell et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
- (2013) Nicola Segata et al. Nature Communications
- EMPeror: a tool for visualizing high-throughput microbial community data
- (2013) Yoshiki Vázquez-Baeza et al. GigaScience
- The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates
- (2012) Julien Soubrier et al. MOLECULAR BIOLOGY AND EVOLUTION
- Phylogenomics of Prokaryotic Ribosomal Proteins
- (2012) Natalya Yutin et al. PLoS One
- Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks
- (2012) Daniel H. Huson et al. SYSTEMATIC BIOLOGY
- How stands the Tree of Life a century and a half after The Origin?
- (2011) Maureen A O'Malley et al. Biology Direct
- The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
- (2011) A. R. Nabhan et al. BRIEFINGS IN BIOINFORMATICS
- An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
- (2011) Daniel McDonald et al. ISME Journal
- The NCBI Taxonomy database
- (2011) S. Federhen NUCLEIC ACIDS RESEARCH
- Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer
- (2011) Christopher J. Creevey et al. PLoS One
- The archaeal ‘TACK’ superphylum and the origin of eukaryotes
- (2011) Lionel Guy et al. TRENDS IN MICROBIOLOGY
- Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
- (2011) Hervé Philippe et al. PLOS BIOLOGY
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- Genome Networks Root the Tree of Life between Prokaryotic Domains
- (2010) Tal Dagan et al. Genome Biology and Evolution
- Rooting the Ribosomal Tree of Life
- (2010) G. P. Fournier et al. MOLECULAR BIOLOGY AND EVOLUTION
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- (2010) Morgan N. Price et al. PLoS One
- The Modern Concept of the Procaryote
- (2009) W. B. Whitman JOURNAL OF BACTERIOLOGY
- Genome beginnings: rooting the tree of life
- (2009) J. A. Lake et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont
- (2009) John P. McCutcheon et al. PLoS Genetics
- Empirical profile mixture models for phylogenetic reconstruction
- (2008) Le Si Quang et al. BIOINFORMATICS
- The conditioned reconstructed process
- (2008) Tanja Gernhard JOURNAL OF THEORETICAL BIOLOGY
- An Improved General Amino Acid Replacement Matrix
- (2008) S. Q. Le et al. MOLECULAR BIOLOGY AND EVOLUTION
- Broad phylogenomic sampling improves resolution of the animal tree of life
- (2008) Casey W. Dunn et al. NATURE
- The archaebacterial origin of eukaryotes
- (2008) C. J. Cox et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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