A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
2016
Nucleic Acids Research
Preserved Fulltext
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]
2018
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2015
PeerJ
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2016; you can also visit the original URL.
The file type is application/pdf.
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
2012
BMC Bioinformatics
Preserved Fulltext
The Internet Archive has a preservation copy of this work in our general collections.
The file type is application/pdf.
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]
2018
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2017
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2019
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2013
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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]
2019
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2020
Mycosphere
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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]
2017
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2018
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2021
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2017
Current Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2017
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 196 results