Letunic I, Bork P.. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: 127-128

EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
Bioinformatics (Impact Factor: 4.98). 02/2007; 23(1):127-8. DOI: 10.1093/bioinformatics/btl529
Source: PubMed


Interactive Tree Of Life (iTOL) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. Trees
can be interactively pruned and re-rooted. Various types of data such as genome sizes or protein domain repertoires can be
mapped onto the tree. Export to several bitmap and vector graphics formats is supported.

Availability: iTOL is available at

Contact: bork{at}

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    • "for visualization (Waterhouse et al., 2009). This alignment was used to construct a phylogenetic tree using the maximum likelihood method (PhyML software; Guindon et al., 2005; Guindon and Gascuel, 2003) and transferred to the iToL server for visualization (Letunic and Bork, 2007). Bootstrap values are expressed as percentages of 100 replicates. "
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    ABSTRACT: Histidine kinase receptors (HKRs) appear to be a common strategy for model and pathogenic fungi to sense and respond to environmental stresses. In the human pathogen Aspergillus fumigatus, which is responsible for invasive aspergillosis, 13 genes potentially encoding HKRs have been identified. Until now, only three HKRs have been functionally characterized. The aim of this study was to perform the systematic invalidation of A. fumigatus HKR genes and the careful phenotypic characterization of the relevant mutants. This study notably allowed to gain new important insights into the role of HKRs in physiology of A. fumigatus. Actually, we showed that (i) NikA/TcsC could be involved in the cell wall integrity pathway, (ii) Fhk6 and PhkA were involved in the regulation of the "fluffy" developmental program, (iii) PhkB could participate in the regulation of conidiation and (iv) PhkA was implied in the resistance of oxidative stresses.
    Fungal Genetics and Biology 09/2015; DOI:10.1016/j.fgb.2015.09.005 · 2.59 Impact Factor
    • "For the construction of the MCG tree, phylogenetic inference was carried out with RAxML version 7.7.1 (Stamatakis et al., 2008) that estimates large phylogenies by maximum likelihood. The best phylogenetic tree estimated by the GTRCAT model with 1000 bootstrap replicates was drawn with iTOL (Letunic and Bork, 2007). "
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    ABSTRACT: Members of the archaeal Miscellaneous Crenarchaeotic Group (MCG) are among the most successful microorganisms on the planet. During its evolutionary diversification, this very diverse group has managed to cross the saline-freshwater boundary, one of the most important evolutionary barriers structuring microbial communities. However, the current understanding on the ecological significance of MCG in freshwater habitats is scarce and the evolutionary relationships between freshwater and saline MCG remains poorly known. Here, we carried out molecular phylogenies using publicly available 16S rRNA gene sequences from various geographic locations to investigate the distribution of MCG in freshwater and saline sediments and to evaluate the implications of saline-freshwater transitions during the diversification events. Our approach provided a robust ecological framework in which MCG archaea appeared as a core generalist group in the sediment realm. However, the analysis of the complex intragroup phylogeny of the 21 subgroups currently forming the MCG lineage revealed that distinct evolutionary MCG subgroups have arisen in marine and freshwater sediments suggesting the occurrence of adaptive evolution specific to each habitat. The ancestral state reconstruction analysis indicated that this segregation was mainly due to the occurrence of a few saline-freshwater transition events during the MCG diversification. In addition, a network analysis showed that both saline and freshwater MCG recurrently co-occur with archaea of the class Thermoplasmata in sediment ecosystems, suggesting a potentially relevant trophic connection between the two clades.The ISME Journal advance online publication, 18 August 2015; doi:10.1038/ismej.2015.143.
    The ISME Journal 08/2015; DOI:10.1038/ismej.2015.143 · 9.30 Impact Factor
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    • "Anaerobes undoubtedly play a major role in the pathophysiology in CF patients because they are involved in inflammation, Fig. 1 Phylogenetic tree of the bacterial diversity of core CF pulmonary microbiota. This figure was created using the interactive Tree Of Life (iTOL) (Letunic and Bork 2007). The inner circle shows genera colored by phylum or Proteobacteria class. "
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    ABSTRACT: Pseudomonas aeruginosa plays a major role in cystic fibrosis (CF) progression. Therefore, it is important to understand the initial steps of P. aeruginosa infection. The structure and dynamics of CF respiratory tract microbial communities during the early stages of P. aeruginosa colonization were characterized by pyrosequencing and cloning‑sequencing. The respiratory microbiota showed high diversity, related to the young age of the CF cohort (mean age 10 years). Wide inter‑ and intra‑individual variations were revealed. A common core microbiota of 5 phyla and 13 predominant genera was found, the majority of which were obligate anaerobes. A few genera were significantly more prevalent in patients never infected by P. aeruginosa. Persistence of an anaerobic core microbiota regardless of P. aeruginosa status suggests a major role of certain anaerobes in the pathophysiology of lung infections in CF. Some genera may be potential biomarkers of pulmonary infection state.
    SpringerPlus 08/2015; 4(1). DOI:10.1186/s40064-015-1207-0
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