ALBERT

Description: The post-translational regulation of proteins is mainly driven by two molecular events, their modification by several types of moieties and their interaction with other proteins. These two processes are interdependent and together are responsible for the function of the protein in a particular cell state. Several databases focus on the prediction and compilation of protein–protein interactions (PPIs) and no less on the collection and analysis of protein post-translational modifications (PTMs), however, there are no resources that concentrate on describing the regulatory role of PTMs in PPIs. We developed several methods based on residue co-evolution and proximity to predict the functional associations of pairs of PTMs that we apply to modifications in the same protein and between two interacting proteins. In order to make data available for understudied organisms, PTMcode v2 ( http://ptmcode.embl.de ) includes a new strategy to propagate PTMs from validated modified sites through orthologous proteins. The second release of PTMcode covers 19 eukaryotic species from which we collected more than 300 000 experimentally verified PTMs (〉1 300 000 propagated) of 69 types extracting the post-translational regulation of 〉100 000 proteins and 〉100 000 interactions. In total, we report 8 million associations of PTMs regulating single proteins and over 9.4 million interplays tuning PPIs.

Description: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jarvis, Erich D -- Mirarab, Siavash -- Aberer, Andre J -- Li, Bo -- Houde, Peter -- Li, Cai -- Ho, Simon Y W -- Faircloth, Brant C -- Nabholz, Benoit -- Howard, Jason T -- Suh, Alexander -- Weber, Claudia C -- da Fonseca, Rute R -- Li, Jianwen -- Zhang, Fang -- Li, Hui -- Zhou, Long -- Narula, Nitish -- Liu, Liang -- Ganapathy, Ganesh -- Boussau, Bastien -- Bayzid, Md Shamsuzzoha -- Zavidovych, Volodymyr -- Subramanian, Sankar -- Gabaldon, Toni -- Capella-Gutierrez, Salvador -- Huerta-Cepas, Jaime -- Rekepalli, Bhanu -- Munch, Kasper -- Schierup, Mikkel -- Lindow, Bent -- Warren, Wesley C -- Ray, David -- Green, Richard E -- Bruford, Michael W -- Zhan, Xiangjiang -- Dixon, Andrew -- Li, Shengbin -- Li, Ning -- Huang, Yinhua -- Derryberry, Elizabeth P -- Bertelsen, Mads Frost -- Sheldon, Frederick H -- Brumfield, Robb T -- Mello, Claudio V -- Lovell, Peter V -- Wirthlin, Morgan -- Schneider, Maria Paula Cruz -- Prosdocimi, Francisco -- Samaniego, Jose Alfredo -- Vargas Velazquez, Amhed Missael -- Alfaro-Nunez, Alonzo -- Campos, Paula F -- Petersen, Bent -- Sicheritz-Ponten, Thomas -- Pas, An -- Bailey, Tom -- Scofield, Paul -- Bunce, Michael -- Lambert, David M -- Zhou, Qi -- Perelman, Polina -- Driskell, Amy C -- Shapiro, Beth -- Xiong, Zijun -- Zeng, Yongli -- Liu, Shiping -- Li, Zhenyu -- Liu, Binghang -- Wu, Kui -- Xiao, Jin -- Yinqi, Xiong -- Zheng, Qiuemei -- Zhang, Yong -- Yang, Huanming -- Wang, Jian -- Smeds, Linnea -- Rheindt, Frank E -- Braun, Michael -- Fjeldsa, Jon -- Orlando, Ludovic -- Barker, F Keith -- Jonsson, Knud Andreas -- Johnson, Warren -- Koepfli, Klaus-Peter -- O'Brien, Stephen -- Haussler, David -- Ryder, Oliver A -- Rahbek, Carsten -- Willerslev, Eske -- Graves, Gary R -- Glenn, Travis C -- McCormack, John -- Burt, Dave -- Ellegren, Hans -- Alstrom, Per -- Edwards, Scott V -- Stamatakis, Alexandros -- Mindell, David P -- Cracraft, Joel -- Braun, Edward L -- Warnow, Tandy -- Jun, Wang -- Gilbert, M Thomas P -- Zhang, Guojie -- DP1 OD000448/OD/NIH HHS/ -- DP1OD000448/OD/NIH HHS/ -- R24 GM092842/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn. ; Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. ; Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. College of Medicine and Forensics, Xi'an Jiaotong University Xi'an 710061, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia. ; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. ; CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Universite Montpellier II Montpellier, France. ; Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA. ; Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. ; Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa 904-0495, Japan. ; Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. ; Laboratoire de Biometrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Universite de Lyon, F-69622 Villeurbanne, France. ; Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avancats, Barcelona, Spain. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. ; Joint Institute for Computational Sciences, The University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. ; Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark. ; The Genome Institute, Washington University School of Medicine, St Louis, MI 63108, USA. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA. ; Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA. ; Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK. ; Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK. Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. ; International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK. ; College of Medicine and Forensics, Xi'an Jiaotong University Xi'an, 710061, China. ; State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China. ; Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA. Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. ; Center for Zoo and Wild Animal Health, Copenhagen Zoo Roskildevej 38, DK-2000 Frederiksberg, Denmark. ; Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. ; Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA. Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. ; Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA. ; Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Biological Sciences, Federal University of Para, Belem, Para, Brazil. ; Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil. ; Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark. ; Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates. ; Dubai Falcon Hospital, Dubai, United Arab Emirates. ; Canterbury Museum Rolleston Avenue, Christchurch 8050, New Zealand. ; Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia. ; Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. ; Laboratory of Genomic Diversity, National Cancer Institute Frederick, MD 21702, USA. Institute of Molecular and Cellular Biology, SB RAS and Novosibirsk State University, Novosibirsk, Russia. ; Smithsonian Institution National Museum of Natural History, Washington, DC 20013, USA. ; BGI-Shenzhen, Shenzhen 518083, China. ; Department of Biological Sciences, National University of Singapore, Republic of Singapore. ; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Suitland, MD 20746, USA. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. ; Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK. ; Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA. ; Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA. ; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004. Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA. ; Center for Biomolecular Science and Engineering, UCSC, Santa Cruz, CA 95064, USA. ; San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA. ; Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA. ; Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, CA 90041, USA. ; Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK. ; Swedish Species Information Centre, Swedish University of Agricultural Sciences Box 7007, SE-750 07 Uppsala, Sweden. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. ; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA. ; Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany. ; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA. ; Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA. ; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. ; Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn. ; BGI-Shenzhen, Shenzhen 518083, China. Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Medicine, University of Hong Kong, Hong Kong. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25504713" target="_blank"〉PubMed〈/a〉

Description: Fecal microbiota transplantation (FMT) has shown efficacy in treating recurrent Clostridium difficile infection and is increasingly being applied to other gastrointestinal disorders, yet the fate of native and introduced microbial strains remains largely unknown. To quantify the extent of donor microbiota colonization, we monitored strain populations in fecal samples from a recent FMT study on metabolic syndrome patients using single-nucleotide variants in metagenomes. We found extensive coexistence of donor and recipient strains, persisting 3 months after treatment. Colonization success was greater for conspecific strains than for new species, the latter falling within fluctuation levels observed in healthy individuals over a similar time frame. Furthermore, same-donor recipients displayed varying degrees of microbiota transfer, indicating individual patterns of microbiome resistance and donor-recipient compatibilities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Simone S -- Zhu, Ana -- Benes, Vladimir -- Costea, Paul I -- Hercog, Rajna -- Hildebrand, Falk -- Huerta-Cepas, Jaime -- Nieuwdorp, Max -- Salojarvi, Jarkko -- Voigt, Anita Y -- Zeller, Georg -- Sunagawa, Shinichi -- de Vos, Willem M -- Bork, Peer -- New York, N.Y. -- Science. 2016 Apr 29;352(6285):586-9. doi: 10.1126/science.aad8852.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052 Sydney, Australia. ; Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. ; Genomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. ; Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, Netherlands. Diabetes Center, Vrije University Medical Center, 1018 HV Amsterdam, Netherlands. Wallenberg Laboratory, University of Gothenburg, 41345 Gothenburg, Sweden. ; Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland. Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland. ; Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany. Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany. ; Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. bork@embl.de willem.devos@wur.nl sunagawa@embl.de. ; Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland. Laboratory of Microbiology, Wageningen University, 6703 HB Wageningen, Netherlands. Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, 00014 Helsinki, Finland. bork@embl.de willem.devos@wur.nl sunagawa@embl.de. ; Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany. Max Delbruck Centre for Molecular Medicine, 13125 Berlin, Germany. Department of Bioinformatics, Biocenter, University of Wurzburg, 97074 Wurzburg, Germany. bork@embl.de willem.devos@wur.nl sunagawa@embl.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27126044" target="_blank"〉PubMed〈/a〉

Description: eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making nested groups hierarchically consistent. This allows for a better propagation of functional terms across nested OGs and led to the novel annotation of 95 890 previously uncharacterized OGs, increasing overall annotation coverage from 67% to 72%. The functional annotations of OGs have been expanded to also provide Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group. Moreover, eggNOG now provides pairwise orthology relationships within OGs based on analysis of phylogenetic trees. We have also incorporated a framework for quickly mapping novel sequences to OGs based on precomputed HMM profiles. Finally, eggNOG version 4.5 incorporates a novel data set spanning 2605 viral OGs, covering 5228 proteins from 352 viral proteomes. All data are accessible for bulk downloading, as a web-service, and through a completely redesigned web interface. The new access points provide faster searches and a number of new browsing and visualization capabilities, facilitating the needs of both experts and less experienced users. eggNOG v4.5 is available at http://eggnog.embl.de .

Description: : MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes. Availability and Implementation: MOCAT2 is implemented in Perl 5 and Python 2.7, designed for 64-bit UNIX systems and offers support for high-performance computer usage via LSF, PBS or SGE queuing systems; source code is freely available under the GPL3 license at http://mocat.embl.de . Contact : bork@embl.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: The thermophilic fungus Chaetomium thermophilum holds great promise for structural biology. To increase the efficiency of its biochemical and structural characterization and to explore its thermophilic properties beyond those of individual proteins, we obtained transcriptomics and proteomics data, and integrated them with computational annotation methods and a multitude of biochemical experiments conducted by the structural biology community. We considerably improved the genome annotation of Chaetomium thermophilum and characterized the transcripts and expression of thousands of genes. We furthermore show that the composition and structure of the expressed proteome of Chaetomium thermophilum is similar to its mesophilic relatives. Data were deposited in a publicly available repository and provide a rich source to the structural biology community.

Description: The many functional partnerships and interactions that occur between proteins are at the core of cellular processing and their systematic characterization helps to provide context in molecular systems biology. However, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness. The STRING database ( http://string-db.org ) aims to provide a critical assessment and integration of protein–protein interactions, including direct (physical) as well as indirect (functional) associations. The new version 10.0 of STRING covers more than 2000 organisms, which has necessitated novel, scalable algorithms for transferring interaction information between organisms. For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution. Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein–protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis for enrichment tests in user-provided networks.

Description: The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org

Description: With the increasing availability of various ‘omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de ) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families. Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality genomes to minimize error propagation from incomplete proteome sets. Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of high-quality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels compared with 41 in eggNOGv3, (iii) identification and annotation of particularly closely related orthologous groups, facilitating analysis of related gene families, (iv) improvements of the clustering and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures throughout the entire pipeline. As in previous versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. Users can access the complete database of orthologous groups via a web interface, as well as through bulk download.

Description: Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and paralogy relationships, and in the detection of relevant evolutionary events such as gene family expansions and contractions, horizontal gene transfer, recombination or incomplete lineage sorting. Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes). Here, we introduce a new release of PhylomeDB ( http://phylomedb.org ), a public repository of phylomes. Currently, PhylomeDB hosts 120 public phylomes, comprising 〉1.5 million maximum likelihood trees and multiple sequence alignments. In the current release, phylogenetic trees are annotated with taxonomic, protein-domain arrangement, functional and evolutionary information. PhylomeDB is also a major source for phylogeny-based predictions of orthology and paralogy, covering 〉10 million proteins across 1059 sequenced species. Here we describe newly implemented PhylomeDB features, and discuss a benchmark of the orthology predictions provided by the database, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes.