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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    • "The alignment was filtered using the greengenes lanemask. Phylogenetic analysis was performed using FastTree (Price, Dehal and Arkin 2010), and the online tool iTOL was used for tree visualization (Letunic and Bork 2007). The OTU map generated in QIIME using the result of usearch qf was used for further diversity analyses. "
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    ABSTRACT: The springtail Folsomia candida is an important model organism for soil ecology, ecotoxicology and ecogenomics. The decomposer activities of soil invertebrates like Folsomia depend on their relationship with microbial communities including gut symbionts. In this paper, we apply high-throughput sequencing to provide a detailed characterization of the bacterial community associated with parthenogenetic F. candida. First, we evaluated a method to suppress the amplification of DNA from the endosymbiont Wolbachia, to prevent it from interfering with the identification of less abundant Operational Taxonomic Units (OTUs). The suppression treatment applied was effective against Wolbachia and did not interfere with the detection of the most abundant OTUs (59 OTUs, contributing over 87% of the reads). However, this method did affect the inferred community composition. Significant differences were subsequently observed in the composition of bacterial communities associated with two different strains of F. candida. A total of 832 OTUs were found, of which 45% were only present in one strain and 17% only in the other. Among the 20 most abundant OTUs 16 were shared between strains. Denaturing Gradient Gel Electrophoresis (DGGE) and clone libraries, although unable to capture the full diversity of the bacterial community, provided results that supported the NGS data.
    FEMS Microbiology Ecology 10/2015; DOI:10.1093/femsec/fiv128 · 3.57 Impact Factor
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    • ", 2014 ) . The dendrograms were created in Mega6 and edited in iTOL ( Letunic and Bork , 2007 ; Tamura et al . , 2013 ) . "
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    ABSTRACT: Multiple studies confirm laccase role in fungal pathogenicity and lignocellulose degradation. In spite of broad genomic research, laccases from plant wilt pathogen Fusarium oxysporum are still not characterized. The study aimed to identify F. oxysporum genes that may encode laccases sensu stricto and to characterize the proteins in silico in order to facilitate further research on their impact on the mentioned processes. Twelve sequenced F. oxysporum genomes available on Broad Institute of Harvard and MIT (2015) website were analyzed and three genes that may encode laccases sensu stricto were found. Their amino acid sequences possess all features essential for their catalytic activity, moreover, the homology models proved the characteristic 3D laccase structures. The study shades light on F. oxysporum as a new source of multicopper oxidases, enzymes with possible high redox potential and broad perspective in biotechnological applications.
    Frontiers in Microbiology 10/2015; 6:933. DOI:10.3389/fmicb.2015.00933 · 3.99 Impact Factor
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    • "In the settings , FastTree used JTT model for amino acid substitution and computed local support values with the Shimodaira- Hasegawa test to estimate the reliability of each split in the tree (for more details, please see FastTree User's Guide, http:// Finally, the generated tree data was submitted to iTOL for viewing phylogenetic trees (Letunic and Bork 2007, 2011). "
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    ABSTRACT: Ferritins are highly conserved proteins that are widely distributed in various species from archaea to humans. The ubiquitous characteristic of these proteins reflects the pivotal contribution of ferritins to the safe storage and timely delivery of iron to achieve iron homeostasis. This study investigated the ferritin genes in 248 genomes from various species, including viruses, archaea, bacteria, and eukarya. The distribution comparison suggests that mammals and eudicots possess abundant ferritin genes, whereas fungi contain very few ferritin genes. Archaea and bacteria show considerable numbers of ferritin genes. Generally, prokaryotes possess three types of ferritin (the typical ferritin, bacterioferritin, and DNA-binding protein from starved cell), whereas eukaryotes have various subunit types of ferritin, thereby indicating the individuation of the ferritin family during evolution. The characteristic motif analysis of ferritins suggested that all key residues specifying the unique structural motifs of ferritin are highly conserved across three domains of life. Meanwhile, the characteristic motifs were also distinguishable between ferritin groups, especially phytoferritins, which show a plant-specific motif. The phylogenetic analyses show that ferritins within the same subfamily or subunits are generally clustered together. The phylogenetic relationships among ferritin members suggest that both gene duplication and horizontal transfer contribute to the wide variety of ferritins, and their possible evolutionary scenario was also proposed. The results contribute to a better understanding of the distribution, characteristic motif, and evolutionary relationship of the ferritin family.
    The Science of Nature 10/2015; 102(9-10). DOI:10.1007/s00114-015-1314-3 · 2.10 Impact Factor
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