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Iroki: automatic customization and visualization of phylogenetic trees

https://doi.org/10.1101/106138
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Marine bacterial richness increases towards higher latitudes in the eastern Indian Ocean
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Drawing Phylogenetic Trees
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Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons
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The measurement of diversity in different types of biological collections
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MLweb: A toolkit for machine learning on the web
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The prevalence ofEscherichia coliO157.H7 in dairy and beef cattle in Washington State
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Global marine bacterial diversity peaks at high latitudes in winter
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Effects of environmental variation and spatial distance on Bacteria, Archaea and viruses in sub-polar and arctic waters
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Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases
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Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
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Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans
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Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens
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Open science resources for the discovery and analysis of Tara Oceans data
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Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function
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Enterohaemorrhagic Escherichia coli : emerging issues on virulence and modes of transmission
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Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses
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APE: Analyses of Phylogenetics and Evolution in R language
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Treevolution: visual analysis of phylogenetic trees
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SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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IcyTree: rapid browser-based visualization for phylogenetic trees and networks
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ViPTree: the viral proteomic tree server
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PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization
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Computational approaches to predict bacteriophage–host relationships
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
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Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web
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Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
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EvolView, an online tool for visualizing, annotating and managing phylogenetic trees
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The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
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Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
inferredcites →https://doi.org/10.1093/nar/gkw370openalex-snapshot
Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees
inferredcites →https://doi.org/10.1099/jgv.0.000016openalex-snapshot
Methods for virus classification and the challenge of incorporating metagenomic sequence data
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Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy
inferredcites →https://doi.org/10.1109/tvcg.2011.185openalex-snapshot
D³ Data-Driven Documents
inferredcites →https://doi.org/10.1111/j.1462-2920.2011.02664.xopenalex-snapshot
Sponge‐specific clusters revisited: a comprehensive phylogeny of sponge‐associated microorganisms
inferredcites →https://doi.org/10.1111/j.1574-6941.2011.01054.xopenalex-snapshot
Ecological traits of planktonic viruses and prokaryotes along a full-salinity gradient
inferredcites →https://doi.org/10.1111/j.2041-210x.2011.00169.xopenalex-snapshot
phytools: an R package for phylogenetic comparative biology (and other things)
inferredcites →https://doi.org/10.1111/jam.12250openalex-snapshot
Correlation analysis of Shiga toxin-producingEscherichia colishedding and faecal bacterial composition in beef cattle
inferredcites →https://doi.org/10.1126/science.8511586openalex-snapshot
From RNA to DNA, Why So Many Ribonucleotide Reductases?
inferredcites →https://doi.org/10.1126/science.aac5605openalex-snapshot
Tara Oceans studies plankton at planetary scale
inferredcites →https://doi.org/10.1128/aem.00533-11openalex-snapshot
Biodiversity and Emerging Biogeography of the Neutrophilic Iron-Oxidizing Zetaproteobacteria
inferredcites →https://doi.org/10.1128/aem.01946-13openalex-snapshot
New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake
inferredcites →https://doi.org/10.1128/aem.03006-05openalex-snapshot
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
inferredcites →https://doi.org/10.1128/aem.71.12.8228-8235.2005openalex-snapshot
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
inferredcites →https://doi.org/10.1128/jb.184.16.4529-4535.2002openalex-snapshot
The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage
inferredcites →https://doi.org/10.1128/jb.186.21.7029-7031.2004openalex-snapshot
Phage Taxonomy: We Agree To Disagree
inferredcites →https://doi.org/10.1128/msphere.00359-16openalex-snapshot
Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean
inferredcites →https://doi.org/10.1146/annurev-biochem-061408-095817openalex-snapshot
Class I Ribonucleotide Reductases: Metallocofactor Assembly and Repair In Vitro and In Vivo
inferredcites →https://doi.org/10.1146/annurev.biochem.75.103004.142443openalex-snapshot
Ribonucleotide Reductases
inferredcites →https://doi.org/10.1186/1471-2105-10-356openalex-snapshot
phyloXML: XML for evolutionary biology and comparative genomics
inferredcites →https://doi.org/10.1186/1471-2105-11-7openalex-snapshot
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
inferredcites →https://doi.org/10.1186/1471-2105-12-63openalex-snapshot
BIO::Phylo-phyloinformatic analysis using perl
inferredcites →https://doi.org/10.1186/1471-2105-13-209openalex-snapshot
Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython
inferredcites →https://doi.org/10.1186/1471-2105-8-460openalex-snapshot
Dendroscope: An interactive viewer for large phylogenetic trees
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A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes
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ColorTree: a batch customization tool for phylogenic trees
inferredcites →https://doi.org/10.1186/2047-217x-1-7openalex-snapshot
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
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An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform
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treeman: an R package for efficient and intuitive manipulation of phylogenetic trees
inferredcites →https://doi.org/10.1186/s40168-016-0155-4openalex-snapshot
Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides
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Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains
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Deep Neural Networks as a Computational Model for Human Shape Sensitivity
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PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories
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Genetic Architecture of Skin and Eye Color in an African-European Admixed Population
inferredcites →https://doi.org/10.1371/journal.pgen.1003987openalex-snapshot
Expanding the Marine Virosphere Using Metagenomics
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FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
inferredcites →https://doi.org/10.1371/journal.pone.0016329openalex-snapshot
Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution
inferredcites →https://doi.org/10.1371/journal.pone.0098115openalex-snapshot
Escherichia coli O157:H7 Super-Shedder and Non-Shedder Feedlot Steers Harbour Distinct Fecal Bacterial Communities
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Salinity Regulation of the Interaction of Halovirus SNJ1 with Its Host and Alteration of the Halovirus Replication Strategy to Adapt to the Variable Ecosystem
inferredcites →https://doi.org/10.1371/journal.pone.0170050openalex-snapshot
Changes in bacterial community composition of Escherichia coli O157:H7 super-shedder cattle occur in the lower intestine
inferredcites →https://doi.org/10.3389/fmicb.2015.00656openalex-snapshot
Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions
inferredcites →https://doi.org/10.3389/fmicb.2016.00337openalex-snapshot
Composition and Interactions among Bacterial, Microeukaryotic, and T4-like Viral Assemblages in Lakes from Both Polar Zones
inferredcites →https://doi.org/10.3389/fmicb.2019.00134openalex-snapshot
Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton
inferredcites →https://doi.org/10.3389/fmicb.2019.00167openalex-snapshot
The Environment and Cyanophage Diversity: Insights From Environmental Sequencing of DNA Polymerase
inferredcites →https://doi.org/10.3390/v8010022openalex-snapshot
Innate Immunity Evasion by Enteroviruses: Insights into Virus-Host Interaction
inferredcites →https://doi.org/10.3390/v8030066openalex-snapshot
Linking Virus Genomes with Host Taxonomy
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VIROME: a standard operating procedure for analysis of viral metagenome sequences
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A colour scheme for the display of astronomical intensity images
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JPhyloIO - A Java library for event-based reading and writing of different alignment and tree formats through one common interface
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Ventromedial hypothalamic neurons control a defensive emotion state
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Compact graphical representation of phylogenetic data and metadata with GraPhlAn

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Genome-wide genetic diversity is maintained through decades of soybean breeding in Canada
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inferred← citeshttps://doi.org/10.1128/jb.00740-18openalex-snapshot
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Uncovering superior alleles and genetic loci for yield-related traits in mungbean (Vigna radiata L. Wilczek) through a genome-wide association study
inferred← citeshttps://doi.org/10.1371/journal.pone.0260714openalex-snapshot
Patient health records and whole viral genomes from an early SARS-CoV-2 outbreak in a Quebec hospital reveal features associated with favorable outcomes
inferred← citeshttps://doi.org/10.3389/fmicb.2018.02528openalex-snapshot
Bacterial Diversity and the Geochemical Landscape in the Southwestern Gulf of Mexico
inferred← citeshttps://doi.org/10.3389/fmicb.2018.03053openalex-snapshot
Family A DNA Polymerase Phylogeny Uncovers Diversity and Replication Gene Organization in the Virioplankton
inferred← citeshttps://doi.org/10.3389/fmicb.2019.00134openalex-snapshot
Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton
inferred← citeshttps://doi.org/10.3389/fmicb.2020.00843openalex-snapshot
Global Distribution and Evolution of Mycobacterium bovis Lineages
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