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Protocols

iTOL specifications

Information


Unique identifier OMICS_04256
Name iTOL
Alternative name interactive Tree Of Life
Interface Web user interface
Restrictions to use None
Input format Nexus, Newick, phyloXML
Computer skills Basic
Version 4.0
Stability Stable
Maintained Yes

Maintainers


  • person_outline Ivica Letunic
  • person_outline Bork Peer

Publications for interactive Tree Of Life

iTOL citations

 (1057)
library_books

Regulatory protein SrpA controls phage infection and core cellular processes in Pseudomonas aeruginosa

2018
Nat Commun
PMCID: 5945682
PMID: 29748556
DOI: 10.1038/s41467-018-04232-6

[…] tic tree of the 16s rRNA gene sequences from 2156 strains by searching the genome database of Pseudomonas using a software MEGA7. The phylogenetic trees were modified using an online software (http://itol.embl.de/). […]

library_books

Detection of Chlamydiaceae and Chlamydia like organisms on the ocular surface of children and adults from a trachoma endemic region

2018
Sci Rep
PMCID: 5943520
PMID: 29743637
DOI: 10.1038/s41598-018-23887-1

[…] ateway,. The partial 16S rRNA gene sequences obtained in this study were added subsequently to the Bayesian tree using the Quick-Add Parsimony option in ARB. The phylogenetic tree was visualized with iTOL and FigTree, (Fig. ).Second, all obtained consensus sequences as well as the 16S rRNA gene sequences of C. trachomatis A/Har-13T (A_E17344.1), C. caviae strain: Gp/Ic (=ATCC VR813) (D85708.1), N. […]

call_split

What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs

2018
PMCID: 5956146
PMID: 29743201
DOI: 10.1128/mSphere.00122-18
call_split See protocol

[…] reference sequence database (RefSeq, NCBI, release 82) prefiltered for Archaea using ClustalX version 2.1 () and MEGA version 7.0 (). The maximum likelihood tree was visualized and modified using the interactive Tree of Life platform (iTOL, version 3) (). […]

library_books

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

2018
Front Microbiol
PMCID: 5945981
PMID: 29780368
DOI: 10.3389/fmicb.2018.00836

[…] istances among different strains and the generated distances were employed in Unweighted Pair Group Method with Arithmetic mean (UPGMA) clustering. The generated UPGMA tree files were exported to the Interactive Tree of Life (iTOL) software (Letunic and Bork, ) for viewing and editing. The identified RE-2010 sequences in S. Enteritidis genomes from known outbreaks (n = 111) were extracted from PHA […]

library_books

Gut microbiomes of wild great apes fluctuate seasonally in response to diet

2018
Nat Commun
PMCID: 5934369
PMID: 29725011
DOI: 10.1038/s41467-018-04204-w

[…] eneral time reversible substitution model with a gamma distribution and invariant site correction for rate heterogeneity (GTR + i + Γ) were generated using MEGA7. Phylogenies were annotated using the Interactive Tree of Life. […]

library_books

Comparative genomics of cocci shaped Sporosarcina strains with diverse spatial isolation

2018
BMC Genomics
PMCID: 5930826
PMID: 29716534
DOI: 10.1186/s12864-018-4635-8

[…] re when aligning sequences []. FastTree2 was used to build a phylogenetic tree using GTR + gamma20 parameters and 1000 bootstrap replicates []. Tree visualization was done using the web-based program interactive Tree of Life (iTOL) []. […]

Citations

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iTOL institution(s)
EMBL, Heidelberg, Germany

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