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Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Ivica Letunic, Peer Bork
2016 Nucleic Acids Research  
Interactive Tree Of Life (http://itol.embl.de) is a webbased tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone.  ...  Full interactive control over precise positioning of various annotation features and an unlimited number of datasets allow the easy creation of complex tree visualizations. iTOL 3 is the first tool which  ...  INTRODUCTION Phylogenetics and phylogenetic trees are important concepts and tools in a wide variety of biological and other scientific studies.  ... 
doi:10.1093/nar/gkw290 pmid:27095192 pmcid:PMC4987883 fatcat:sapmktuxyvexzecau5yvbn6gl4

PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies [article]

Dong Zhang, Fangluan Gao, Wen X Li, Ivan Jakovlić, Hong Zou, Jin Zhang, Gui T Wang
2018 bioRxiv   pre-print
It employs a plugin-based system that integrates a number of useful phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation  ...  Multi-gene and genomic datasets have become commonplace in the field of phylogenetics, but many of the existing tools are not designed for such datasets, which makes the analysis time-consuming and tedious  ...  Acknowledgements 156 The authors would like to thank Dr. Xiao-Qin Xia for modifying the manuscript and  ... 
doi:10.1101/489088 fatcat:6655xsuobfhebhe2clfq4rafqq

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

Francesco Asnicar, George Weingart, Timothy L. Tickle, Curtis Huttenhower, Nicola Segata
2015 PeerJ  
It can be executed either locally or through an online Galaxy web application.  ...  We developed GraPhlAn (Graphical Phylogenetic Analysis), a computational tool that produces high-quality, compact visualizations of microbial genomes and metagenomes.  ...  ACKNOWLEDGEMENTS We would like to thank the members of the Segata and Huttenhower labs for helpful suggestions, the WebValley team and participants for inspiring comments and tests, and the users that  ... 
doi:10.7717/peerj.1029 pmid:26157614 pmcid:PMC4476132 fatcat:zcgu4mbnozhfrbozu25iokwul4

The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences

Kevin Riehle, Cristian Coarfa, Andrew Jackson, Jun Ma, Arpit Tandon, Sameer Paithankar, Sriram Raghuraman, Toni-Ann Mistretta, Delphine Saulnier, Sabeen Raza, Maria Diaz, Robert Shulman (+3 others)
2012 BMC Bioinformatics  
The Genboree Microbiome Toolset provides an interactive environment for users at all bioinformatic experience levels in which to conduct microbiome analysis.  ...  Microbial metagenomic analyses rely on an increasing number of publicly available tools.  ...  The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2105/13/S13/S1  ... 
doi:10.1186/1471-2105-13-s13-s11 pmid:23320832 pmcid:PMC3426808 fatcat:atm62tuhabhlddjwcaekjtocrq

Further expansion of methane metabolism in the Archaea [article]

Yulin Wang, Zhengshuang Hua, Kian Mau Goh, Paul N. Evans, Lei Liu, Yanping Mao, Philip Hugenholtz, Gene W. Tyson, Wenjun Li, Tong Zhang
2018 bioRxiv   pre-print
These newly recovered archaea phylogenetically cluster with Geoarchaeota (deep lineage of archaeal order Thermoproteales), and the MCR-encoding genes clustered with the recently reported methanogens within  ...  The recent discovery of key methane-metabolizing genes in the genomes from the archaeal phyla Bathyarchaeota and Verstraetearchaeota has expanded our understanding of the distribution of methane metabolism  ...  Interactive tree of life (iTOL) v3: an online tool for the display 307 and annotation of phylogenetic and other trees.  ... 
doi:10.1101/312082 fatcat:umz4tdnhjzgmxowe7efzieqity

Boosting Felsenstein Phylogenetic Bootstrap [article]

Frederic Lemoine, Jean-Baka Domelevo Entfellner, Eduan Wilkinson, Tulio De Oliveira, Olivier Gascuel
2017 bioRxiv   pre-print
Felsenstein's article describing the application of the bootstrap to evolutionary trees, is one of the most cited papers of all time.  ...  Our method is applied to large simulation, mammal and HIV datasets, for which it reveals the phylogenetic signal, while Felsenstein's bootstrap fails to do so.  ...  Bork, Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nuc. Acids Res. 44, W242-W245 (2016).  ... 
doi:10.1101/154542 fatcat:h4d3oy4zenajbdti4l6ab74plq

A novel phyllosphere resident Protomyces species that interacts with the Arabidopsis immune system [article]

Kai Wang, Timo Sipilä, Sitaram Rajaraman, Omid Safronov, Pia Laine, Agate Auzane, Alfredo Mari, Petri Auvinen, Lars Paulin, Eric Kemen, Jarkko Salojärvi, Kirk Overmyer
2019 bioRxiv   pre-print
phylloplane of wild Arabidopsis thaliana (Arabidopsis), an atypical host.  ...  ABSTRACTWe describe the genome contents of six Protomyces species that are pathogenic within the typical host range of the genus and a novel Protomyces strain (SC29) that was previously isolated from the  ...  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44(W1):W242-W5. 35.  ... 
doi:10.1101/594028 fatcat:yhukajvwsbahlfh3jvyo7zvb3u

eggNOG v4.0: nested orthology inference across 3686 organisms

Sean Powell, Kristoffer Forslund, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Jaime Huerta-Cepas, Toni Gabaldón, Thomas Rattei, Chris Creevey, Michael Kuhn, Lars J. Jensen, Christian von Mering (+1 others)
2013 Nucleic Acids Research  
and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures  ...  Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of highquality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels  ...  ACKNOWLEDGEMENTS The authors wish to thank all members of the Bork group for the fruitful discussions, especially S. Sunagawa and D. Mende for their support.  ... 
doi:10.1093/nar/gkt1253 pmid:24297252 pmcid:PMC3964997 fatcat:tppseymmmbhb5ndnyxnwoktcbq

Marine sediments illuminate Chlamydiae diversity and evolution [article]

Jennah E. Dharamshi, Daniel Tamarit, Laura Eme, Courtney Stairs, Joran Martijn, Felix Homa, Steffen L. Jørgensen, Anja Spang, Thijs J. G. Ettema
2019 bioRxiv   pre-print
Studying environmental chlamydiae, whose genomes display extended metabolic capabilities compared to their pathogenic relatives8-10 has provided first insights into the evolution of the pathogenic and  ...  Here, we report an unprecedented relative abundance and diversity of novel lineages of the Chlamydiae phylum, representing previously undetected, yet potentially important, community members in deep marine  ...  Interactive tree of life (iTOL) v3: an online tool for the display and 836 annotation of phylogenetic and other trees. Nucleic Acids Res 44, W242-245, 837 doi:10.1093/nar/gkw290 (2016). 838 839  ... 
doi:10.1101/577767 fatcat:aaxq44ztivek3kuhmruvvuokzy

Applied aspects of methods to infer phylogenetic relationships amongst fungi

AJ Dissanayake
2020 Mycosphere  
Hence this manuscript is mainly aimed to provide a basic reference or guideline for the mycologists venturing into the field of phylogenetic studies and to avoid unnecessary repetitions in related publications  ...  This reference manuscript is originally conceived for usage with a set of programs necessary for inference of phylogenetic analyses in fungal research (taxonomy and phylogeny).  ...  Hyde for his valuable suggestions to shape the paper and Dr. Martin Ryberg is thanked for providing comments to improve it. Dhanushka N. Wanasinghe, Chada Norphanphoun and Milan C.  ... 
doi:10.5943/mycosphere/11/1/18 fatcat:gz6iinpo55debgebotua5idnam

Complete mitochondrial genome of golden silk producer Antheraea assamensis and its comparative analysis with other lepidopteran insects [article]

Deepika Singh, Debajyoti Kabiraj, Hasnahana Chetia, Pragya Sharma, Kartik Neog, Utpal Bora
2017 bioRxiv   pre-print
Muga (Antheraea assamensis) is an economically important silkmoth endemic to North-eastern part of India and is the producer of the strongest known commercial silk.  ...  The control region contained a six bp deletion atypical of other Antheraea species. Phylogenetic position was consistent with the traditional taxonomic classification of Saturniidae.  ...  Acknowledgements The authors thank the Department of Biotechnology, Govt.  ... 
doi:10.1101/110031 fatcat:wq3aqejovfd7pjfacxbirwoxri

Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria [article]

David Colatriano, Patricia Tran, Celine Gueguen, Williams Williams, Connie Lovejoy, David Walsh
2018 bioRxiv   pre-print
Moreover, an increase in freshwater runoff and riverine transport of organic matter to the Arctic Ocean is a predicted consequence of thawing permafrost and increased precipitation.  ...  The fate of the terrestrial humic-rich organic material and its impact on the marine carbon cycle are largely unknown.  ...  13 The authors declare no competing interests. 301  ... 
doi:10.1101/325027 fatcat:ava3rczhl5hrdlvh2zywvqei6e

Phylogenetic study of thermophilic genera Anoxybacillus, Geobacillus, Parageobacillus, and proposal of a new classification Quasigeobacillus gen. nov [article]

Berenice Talamantes-Becerra, Jason Carling, Jochen Blom, Arthur Georges
2021 bioRxiv   pre-print
A total of 113 genomes were selected for phylogenomic metrics including calculation of Average Nucleotide Identity (ANI) and Average Amino acid Identity (AAI), and a maximum likelihood tree was built from  ...  The combined results from the core gene tree and ANI and AAI dendrograms show that the genomes split into two main clades, clade I containing all Geobacillus, all Parageobacillus and some species of Anoxybacillus  ...  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2013;44:W242-W245. doi:10.1093/nar/gkw290. 60.  ... 
doi:10.1101/2021.06.18.449068 fatcat:q6huv4gifvef5jx3ygrhhgtkca

Novel Predators Reshape Holozoan Phylogeny and Reveal the Presence of a Two-Component Signaling System in the Ancestor of Animals

Elisabeth Hehenberger, Denis V. Tikhonenkov, Martin Kolisko, Javier del Campo, Anton S. Esaulov, Alexander P. Mylnikov, Patrick J. Keeling
2017 Current Biology  
To place the new species into a phylogenetic framework, we built on a previously published dataset of 263 genes [8], extensively expanding the taxon sampling for unicellular relatives of animals and also  ...  In Brief Hehenberger et al. describe three novel Holozoa and infer an updated phylogenomic framework for this group, in the course recovering a new lineage.  ...  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44 (W1), W242-W245. 46.  ... 
doi:10.1016/j.cub.2017.06.006 pmid:28648822 fatcat:tue6r2ymf5hpbk7wdpe4rtngrm

Phylogenomic Synteny Network Analysis Reveals an Ancient MADS-Box Transcription Factor Tandem Duplication and Lineage-Specific Transpositions [article]

Tao Zhao, Rens Holmer, Suzanne de Bruijn, Harrold A. van den Burg, Michael Eric Schranz
2017 bioRxiv   pre-print
With the increase of sequenced and assembled plant genomes, we now have the opportunity to use synteny to analyze the dynamics of gene family expansion and contraction across broad phylogenetic groups.  ...  For example, lineage-specific clusters in the Brassicales containing genes that are well-known for their function in controlling flower morphology (AP3 and PI).  ...  Interactive tree of life (iTOL) v3: an online tool for the display 642 and annotation of phylogenetic and other trees. Nucleic Acids Res. 44:W242-W245 643 Lewis, E.B. 1978.  ... 
doi:10.1101/100990 fatcat:lqtgqkzcjvb6nnbj4gkc7wwxba
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