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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 2.1
Stability Stable
Maintained Yes

Maintainer


  • person_outline Ivica Letunic

Publications for interactive Tree Of Life

iTOL citations

 (856)
call_split

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
call_split See protocol

[…] 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/)., one-way anova was used for comparing statistical difference between the groups of experimental data., the rna sequence data have been deposited in the geo database of ncbi […]

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

[…] 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), […]

library_books

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

[…] 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) ()., selected total-community dna samples of the bog vegetation () were sent for sequencing to eurofins mwg operon (ebersberg, germany; […]

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

[…] 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 […]

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

[…] 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) []., to investigate the geographic distribution of the genus sporosarcina, location data was gathered from the earth microbiome project (emp) [] and rdp []. data […]

library_books

Genome based analysis of Carbapenemase producing Klebsiella pneumoniae isolates from German hospital patients, 2008 2014

2018
PMCID: 5930415
PMID: 29744043
DOI: 10.1186/s13756-018-0352-y

[…] snps in regions of annotated phages and transposases were rejected (not shown). trees were illustrated using figtree v1.4.3. (http://tree.bio.ed.ac.uk/software/figtree/; last access: 25/04/2018) and itol v3 (https://itol.embl.de/; last access: 25/04/2018)., raw reads were trimmed applying trimmomatic 16 (version 0.32, parameters: illuminaclip off, maxinfo 50:0.8, leading 3, trailing 3, crop off, […]


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iTOL institution(s)
EMBL, Heidelberg, Germany

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