标题
Iroki: automatic customization and visualization of phylogenetic trees
作者
关键词
-
出版物
PeerJ
Volume 8, Issue -, Pages e8584
出版商
PeerJ
发表日期
2020-02-26
DOI
10.7717/peerj.8584
参考文献
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。- Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton
- (2019) Amelia O. Harrison et al. Frontiers in Microbiology
- The Environment and Cyanophage Diversity: Insights From Environmental Sequencing of DNA Polymerase
- (2019) Jan F. Finke et al. Frontiers in Microbiology
- A virus or more in (nearly) every cell: ubiquitous networks of virus–host interactions in extreme environments
- (2018) Jacob H. Munson-McGee et al. ISME Journal
- Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy
- (2018) Pakorn Aiewsakun et al. JOURNAL OF GENERAL VIROLOGY
- MLweb: A toolkit for machine learning on the web
- (2018) Fabien Lauer NEUROCOMPUTING
- Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens
- (2018) Vivek Srinivas et al. NATURE
- Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
- (2017) Benjamin J Callahan et al. ISME Journal
- Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons
- (2017) Pedro C. Junger et al. MICROBIAL ECOLOGY
- A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits
- (2017) Lucas Czech et al. MOLECULAR BIOLOGY AND EVOLUTION
- Virus taxonomy in the age of metagenomics
- (2017) Peter Simmonds et al. NATURE REVIEWS MICROBIOLOGY
- Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans
- (2017) Felipe H. Coutinho et al. Nature Communications
- Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean
- (2017) Yosuke Nishimura et al. mSphere
- Changes in bacterial community composition of Escherichia coli O157:H7 super-shedder cattle occur in the lower intestine
- (2017) Rahat Zaheer et al. PLoS One
- Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific
- (2016) Alyse A Larkin et al. ISME Journal
- ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
- (2016) Jaime Huerta-Cepas et al. MOLECULAR BIOLOGY AND EVOLUTION
- Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web
- (2016) Oscar Robinson et al. MOLECULAR BIOLOGY AND EVOLUTION
- Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
- (2016) Simon Roux et al. NATURE
- Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees
- (2016) Zilong He et al. NUCLEIC ACIDS RESEARCH
- 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
- Linking Virus Genomes with Host Taxonomy
- (2016) Tomoko Mihara et al. Viruses-Basel
- HostPhinder: A Phage Host Prediction Tool
- (2016) Julia Villarroel et al. Viruses-Basel
- PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories
- (2016) Victor Hanson-Smith et al. PLoS Computational Biology
- Composition and Interactions among Bacterial, Microeukaryotic, and T4-like Viral Assemblages in Lakes from Both Polar Zones
- (2016) Aguirre de Cárcer Daniel et al. Frontiers in Microbiology
- Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides
- (2016) Jessica Chopyk et al. Microbiome
- Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains
- (2016) Yemin Lan et al. Microbiome
- Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases
- (2015) Zhiqiang Wu et al. ISME Journal
- Methods for virus classification and the challenge of incorporating metagenomic sequence data
- (2015) Peter Simmonds JOURNAL OF GENERAL VIROLOGY
- Counts and sequences, observations that continue to change our understanding of viruses in nature
- (2015) K. Eri Wommack et al. JOURNAL OF MICROBIOLOGY
- Tara Oceans studies plankton at planetary scale
- (2015) P. Bork et al. SCIENCE
- Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function
- (2015) Shengyong Mao et al. Scientific Reports
- Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions
- (2015) Christopher M. Bellas et al. Frontiers in Microbiology
- Compact graphical representation of phylogenetic data and metadata with GraPhlAn
- (2015) Francesco Asnicar et al. PeerJ
- Open science resources for the discovery and analysis of Tara Oceans data
- (2015) Stéphane Pesant et al. Scientific Data
- Salinity Regulation of the Interaction of Halovirus SNJ1 with Its Host and Alteration of the Halovirus Replication Strategy to Adapt to the Variable Ecosystem
- (2015) Yunjun Mei et al. PLoS One
- Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases
- (2014) Albert Leopold Müller et al. ISME Journal
- Escherichia coli O157:H7 Super-Shedder and Non-Shedder Feedlot Steers Harbour Distinct Fecal Bacterial Communities
- (2014) Yong Xu et al. PLoS One
- Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses
- (2014) E. G. Sakowski et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform
- (2014) Douglas W Fadrosh et al. Microbiome
- New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake
- (2013) Joanne B. Emerson et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes
- (2013) Bhakti Dwivedi et al. BMC EVOLUTIONARY BIOLOGY
- Effects of environmental variation and spatial distance on Bacteria, Archaea and viruses in sub-polar and arctic waters
- (2013) Christian Winter et al. ISME Journal
- Global marine bacterial diversity peaks at high latitudes in winter
- (2013) Joshua Ladau et al. ISME Journal
- Correlation analysis of Shiga toxin-producingEscherichia colishedding and faecal bacterial composition in beef cattle
- (2013) L. Zhao et al. JOURNAL OF APPLIED MICROBIOLOGY
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
- (2013) K. Katoh et al. MOLECULAR BIOLOGY AND EVOLUTION
- Expanding the Marine Virosphere Using Metagenomics
- (2013) Carolina Megumi Mizuno et al. PLoS Genetics
- SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
- (2012) Elmar Pruesse et al. BIOINFORMATICS
- Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython
- (2012) Eric Talevich et al. BMC BIOINFORMATICS
- The electrical conductivity of seawater at high temperatures and salinities
- (2012) Rich Pawlowicz DESALINATION
- Role of Arginine 293 and Glutamine 288 in Communication between Catalytic and Allosteric Sites in Yeast Ribonucleotide Reductase
- (2012) Md. Faiz Ahmad et al. JOURNAL OF MOLECULAR BIOLOGY
- The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
- (2012) Christian Quast et al. NUCLEIC ACIDS RESEARCH
- VIROME: a standard operating procedure for analysis of viral metagenome sequences
- (2012) K. Eric Wommack et al. Standards in Genomic Sciences
- The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
- (2012) Daniel McDonald et al. GigaScience
- Class I Ribonucleotide Reductases: Metallocofactor Assembly and Repair In Vitro and In Vivo
- (2011) Joseph A. Cotruvo et al. Annual Review of Biochemistry
- BIO::Phylo-phyloinformatic analysis using perl
- (2011) Rutger A Vos et al. BMC BIOINFORMATICS
- Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms
- (2011) Rachel L. Simister et al. ENVIRONMENTAL MICROBIOLOGY
- Ecological traits of planktonic viruses and prokaryotes along a full-salinity gradient
- (2011) Yvan Bettarel et al. FEMS MICROBIOLOGY ECOLOGY
- D³ Data-Driven Documents
- (2011) M. Bostock et al. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
- Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
- (2011) R. Sanchez et al. NUCLEIC ACIDS RESEARCH
- Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution
- (2011) Welkin H. Pope et al. PLoS One
- phytools: an R package for phylogenetic comparative biology (and other things)
- (2011) Liam J. Revell Methods in Ecology and Evolution
- TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
- (2010) Ben C Stöver et al. BMC BIOINFORMATICS
- QIIME allows analysis of high-throughput community sequencing data
- (2010) J Gregory Caporaso et al. NATURE METHODS
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- (2010) Morgan N. Price et al. PLoS One
- Treevolution: visual analysis of phylogenetic trees
- (2009) R. Santamaria et al. BIOINFORMATICS
- phyloXML: XML for evolutionary biology and comparative genomics
- (2009) Mira V Han et al. BMC BIOINFORMATICS
- Viruses manipulate the marine environment
- (2009) Forest Rohwer et al. NATURE
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExplorePublish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn More