Gearing up to handle the mosaic nature of life in the quest for orthologs

Kristoffer Forslund, Cecile Pereira, Salvador Capella-Gutierrez, Alan Sousa da Silva, Adrian Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, Mateus Patricio, Klaas Vandepoele, Ingo Ebersberger, Judith Blake, Jesualdo Tomás Fernández Breis, Brigitte Boeckmann, Toni Gabaldón, Erik Sonnhammer, Christophe Dessimoz, Suzanna Lewis, Adrian Altenhoff, Carla Bello, Judith Blake, Brigitte Boeckmann, Sébastien Briois, Salvador Capella-Gutierrez, Edward Chalstrey, Hirokazu Chiba, Oscar Conchillo-Solé, Vincent Daubin, Todd DeLuca, Christophe Dessimoz, Jean-Francois Dufayard, Dannie Durand, Ingo Ebersberger, Jesualdo Tomás Fernández-Breis, Kristoffer Forslund, Natasha Glover, Alexander Hauser, Davide Heller, Jaime Huerta-Cepas, Mateusz Kaduk, Jan Koch, Eugene V Koonin, Evgenia Kriventseva, Shigehiro Kuraku, Odile Lecompte, Olivier Lespinet, Jeremy Levy, Suzanna Lewis, Benjamin Liebeskind, Benjamin Linard, Marina Marcet-Houben, Maria Martin, Claire McWhite, Sergei Mekhedov, Sebastien Moretti, Matthieu Muffato, Steven Müller, El-Mabrouk Nadia, Cédric Notredame, Mateus Patricio, Simon Penel, Cécile Pereira, Ivana Pilizota, Henning Redestig, Marc Robinson-Rechavi, Fabian Schreiber, Kimmen Sjölander, Nives Škunca, Erik Sonnhammer, Alan Sousa da Silva, Martin Steinegger, Damian Szklarczyk, Paul Thomas, Ernst Thuer, Clément Train, Ikuo Uchiyama, Klaas Vandepoele, Lucas Wittwer, Ioannis Xenarios, Bethan Yates, Evgeny Zdobnov, Robert M Waterhouse

The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have established a basis to support developments for improved orthology prediction and to explore new approaches. Central to the QfO effort is proper benchmarking of methods and services, as well as design of standardized datasets and standardized formats to allow sharing and comparison of results. Simultaneously, analysis pipelines have been improved, evaluated, and adapted to handle large datasets. All this would not have occurred without the long-term collaboration of Consortium members. Meeting regularly to review and coordinate complementary activities from a broad spectrum of innovative researchers clearly benefits the community. Highlights of the meeting include addressing sources of and legitimacy of disagreements between orthology calls, the context dependency of orthology definitions, special challenges encountered when analyzing very anciently rooted orthologies, orthology in the light of whole-genome duplications, and the concept of orthologous versus paralogous relationships at different levels, including domain-level orthology. Furthermore, particular needs for different applications (e.g. plant genomics, ancient gene families, and others) and the infrastructure for making orthology inferences available (e.g. interfaces with model organism databases) were discussed, with several ongoing efforts that are expected to be reported on during the upcoming 2017 QfO meeting.