TY  - JOUR
A1  - Mende, Daniel R.
A1  - Letunic, Ivica
A1  - Huerta-Cepas, Jaime
A1  - Li, Simone S.
A1  - Forslund, Kristoffer
A1  - Sunagawa, Shinichi
A1  - Bork, Peer
T1  - proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
JF  - Nucleic Acids Research
N2  - The availability of microbial genomes has opened many new avenues of research within microbiology. This has been driven primarily by comparative genomics approaches, which rely on accurate and consistent characterization of genomic sequences. It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades. Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic clade. These genomes are assigned to 5306 consistent and accurate taxonomic species clusters based on previously established methodology. proGenomes also contains functional information for almost 80 million protein-coding genes, including a comprehensive set of general annotations and more focused annotations for carbohydrate-active enzymes and antibiotic resistance genes. Additionally, broad habitat information is provided for many genomes. All genomes and associated information can be downloaded by user-selected clade or multiple habitat-specific sets of representative genomes. We expect that the availability of high-quality genomes with comprehensive functional annotations will promote advances in clinical microbial genomics, functional evolution and other subfields of microbiology. proGenomes is available at http://progenomes.embl.de.
KW  - biology
KW  - genomic sequence
KW  - prokaryotic clade
KW  - proGenomes
KW  - habitat information
KW  - taxonomic description
KW  - genome collection
KW  - comparative genomics
KW  - genomics research
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-171987
VL  - 45
IS  - D1
ER  - 
TY  - JOUR
A1  - Letunic, Ivica
A1  - Bork, Peer
T1  - Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
JF  - Nucleic Acids Research
N2  - 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.
KW  - Interactive Tree Of Life (iTOL)
KW  - phylogenetic trees
KW  - visualization
KW  - tool
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166181
VL  - 44
IS  - W1
ER  -