@article{KoetschanKittelmannLuetal.2014,
  author    = {Koetschan, Christian and Kittelmann, Sandra and Lu, Jingli and Al-Halbouni, Djamila and Jarvis, Graeme N. and M{\"u}ller, Tobias and Wolf, Matthias and Janssen, Peter H.},
  title     = {Internal Transcribed Spacer 1 Secondary Structure Analysis Reveals a Common Core throughout the Anaerobic Fungi (Neocallimastigomycota)},
  series = {PLOS ONE},
  volume    = {9},
  journal   = {PLOS ONE},
  number    = {3},
  doi       = {10.1371/journal.pone.0091928},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-117058},
  pages     = {e91928},
  year      = {2014},
  abstract  = {The internal transcribed spacer (ITS) is a popular barcode marker for fungi and in particular the ITS1 has been widely used for the anaerobic fungi (phylum Neocallimastigomycota). A good number of validated reference sequences of isolates as well as a large number of environmental sequences are available in public databases. Its highly variable nature predisposes the ITS1 for low level phylogenetics; however, it complicates the establishment of reproducible alignments and the reconstruction of stable phylogenetic trees at higher taxonomic levels (genus and above). Here, we overcame these problems by proposing a common core secondary structure of the ITS1 of the anaerobic fungi employing a Hidden Markov Model-based ITS1 sequence annotation and a helix-wise folding approach. We integrated the additional structural information into phylogenetic analyses and present for the first time an automated sequence-structure-based taxonomy of the ITS1 of the anaerobic fungi. The methodology developed is transferable to the ITS1 of other fungal groups, and the robust taxonomy will facilitate and improve high-throughput anaerobic fungal community structure analysis of samples from various environments.},
  language  = {en}
}
@article{LetunicBork2016,
  author    = {Letunic, Ivica and Bork, Peer},
  title     = {Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees},
  series = {Nucleic Acids Research},
  volume    = {44},
  journal   = {Nucleic Acids Research},
  number    = {W1},
  doi       = {10.1093/nar/gkw290},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166181},
  pages     = {W242-W245},
  year      = {2016},
  abstract  = {Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. The current version was completely redesigned and rewritten, utilizing current web technologies for speedy and streamlined processing. Numerous new features were introduced and several new data types are now supported. Trees with up to 100,000 leaves can now be efficiently displayed. Full interactive control over precise positioning of various annotation features and an unlimited number of datasets allow the easy creation of complex tree visualizations. iTOL 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format. Finally, iTOL's account system has been redesigned to simplify the management of trees in user-defined workspaces and projects, as it is heavily used and currently handles already more than 500,000 trees from more than 10,000 individual users.},
  language  = {en}
}
@article{RybalkaWolfAndersenetal.2013,
  author    = {Rybalka, Nataliya and Wolf, Matthias and Andersen, Robert and Friedl, Thomas},
  title     = {Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae)},
  series = {BMC Evolutionary Biology},
  volume    = {13},
  journal   = {BMC Evolutionary Biology},
  number    = {39},
  issn      = {1471-2148},
  doi       = {10.1186/1471-2148-13-39},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121848},
  year      = {2013},
  abstract  = {Background: Heterococcus is a microalgal genus of Xanthophyceae (Stramenopiles) that is common and widespread in soils, especially from cold regions. Species are characterized by extensively branched filaments produced when grown on agarized culture medium. Despite the large number of species described exclusively using light microscopic morphology, the assessment of species diversity is hampered by extensive morphological plasticity. Results: Two independent types of molecular data, the chloroplast-encoded psbA/rbcL spacer complemented by rbcL gene and the internal transcribed spacer 2 of the nuclear rDNA cistron (ITS2), congruently recovered a robust phylogenetic structure. With ITS2 considerable sequence and secondary structure divergence existed among the eight species, but a combined sequence and secondary structure phylogenetic analysis confined to helix II of ITS2 corroborated relationships as inferred from the rbcL gene phylogeny. Intra-genomic divergence of ITS2 sequences was revealed in many strains. The 'monophyletic species concept', appropriate for microalgae without known sexual reproduction, revealed eight different species. Species boundaries established using the molecular-based monophyletic species concept were more conservative than the traditional morphological species concept. Within a species, almost identical chloroplast marker sequences (genotypes) were repeatedly recovered from strains of different origins. At least two species had widespread geographical distributions; however, within a given species, genotypes recovered from Antarctic strains were distinct from those in temperate habitats. Furthermore, the sequence diversity may correspond to adaptation to different types of habitats or climates. Conclusions: We established a method and a reference data base for the unambiguous identification of species of the common soil microalgal genus Heterococcus which uses DNA sequence variation in markers from plastid and nuclear genomes. The molecular data were more reliable and more conservative than morphological data.},
  language  = {en}
}
@article{SchwarzTamuriKultysetal.2016,
  author    = {Schwarz, Roland F. and Tamuri, Asif U. and Kultys, Marek and King, James and Godwin, James and Florescu, Ana M. and Schultz, J{\"o}rg and Goldman, Nick},
  title     = {ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments},
  series = {Nucleic Acids Research},
  volume    = {44},
  journal   = {Nucleic Acids Research},
  number    = {8},
  doi       = {10.1093/nar/gkw022},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166374},
  pages     = {e77},
  year      = {2016},
  abstract  = {Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide consensus-based summaries of the sequences in the alignment. Consequently, individual sequences cannot be identified in the visualization and covariant sites are not easily discernible. We recently proposed Sequence Bundles, a motif visualization technique that maintains a one-to-one relationship between sequences and their graphical representation and visualizes covariant sites. We here present Alvis, an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures. It is available as a full-featured standalone version (http://www.bitbucket.org/rfs/alvis) and its Sequence Bundles visualization module is further available as a web application (http://science-practice.com/projects/sequence-bundles).},
  language  = {en}
}