iTOL pipeline

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 IN pipelines

 (23)
2018
PMCID: 5765115
PMID: 29323230
DOI: 10.1038/s41598-017-18972-w

[…] tonb57 using mafft59, and then concatenating the them. the tree was generated using fasttree60. genomes with identical sets of amr genes are depicted by a single genome. the tree was rendered using itol61., the model and software for predicting mics in for k. pneumoniae genomes can be found at the patric github page: https://github.com/patric3/mic_prediction. all genomes were submitted […]

2018
PMCID: 5831590
PMID: 29490697
DOI: 10.1186/s40168-018-0421-8

[…] gaps [42]. a maximum likelihood phylogeny for the concatenated alignment was conducted using raxml version 8.3.1 under the lg model of evolution with 100 bootstrap replicates [43] and visualized in itol [44]. for sequence-based comparison, average amino acid identity (aai) and average nucleotide identity (ani) values were calculated using the ani and aai calculators from the kostas lab […]

2018
PMCID: 5882874
PMID: 29615754
DOI: 10.1038/s41598-018-23900-7

[…] in some of the late branches and differences in some bootstrap values that do not affect our conclusions. the mapping of riboswitch distribution on the phylogenetic tree was visualized using itol v365. filled shapes (circle for biosynthesis and square for transporter genes) indicate the presence of a riboswitch upstream to the corresponding gene. bootstrap fractions greater than 0.5 […]

2018
PMCID: 5897096
DOI: 10.7554/eLife.33034.033

[…] were midpoint rooted and branches with local support less than 95 were collapsed using the ape and phangorn r packages (paradis et al., 2004; schliep, 2011). phylogenies were visualized using itol version 3.0 (letunic and bork, 2016)., for the data included in figure 2a, the number of genes for which a bacterial origin was confirmed after inspection of the correspondent phylogenetic tree […]

2018
PMCID: 5930944
PMID: 29720179
DOI: 10.1186/s12936-018-2324-3

[…] bootstrap estimation (ufboot) [51] was used with 5000 bootstrap replicates and a best fit model was chosen according to the bayesian inference criterion [52]. phylogenetic trees were visualized with itol [53]., a python package, biostructmap, which allows for the application of a 3d sliding window over a protein structure has been previously described [12]. biostructmap was used to compute […]

iTOL institution(s)
EMBL, Heidelberg, Germany

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