This is the hub for the paper “Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era,. It relates 605 amniote species: 242 placental mammals and 363 avians.
The hub is a combination of data from the Bird 10K and Zoonomia (aka 200 Mammals) projects. The Bird 10K data release paper, Densely sampling genomes across the diversity of birds increases power of comparative genomics analyses. The Bird 10K set contains 363 avian genomes (of which 268 are newly sequenced) as well as alignment, annotation, and conservation data. The 200 Mammals set is referred to in the paper “Genomics in the age of extinction”, in review. The 242 200 Mammals browsers contain alignment and conservation data.
Please see the individual track description pages for details on the data within each track.
Many thanks go to the Bird 10K and 200 Mammals projects, which comprise this combined hub.
Dozens of people from many different institutions contributed to the data available from Bird 10K. A non-exhaustive list includes: Shaohong Feng, Josefin Stiller, Yuan Deng, Joel Armstrong, Qi Fang, Andrew Hart Reeve, Duo Xie, Guangji Chen, Chunxue Guo, Brant Chipstead Faircloth, Bent Petersen, Mark Diekhans, Wan-Jun Chen, Sergio Andreu-Sánchez, Ashot Margaryan, Jason Travis Howard, George Pacheco, Emily Cavill, Mikkel-Holger S. Sinding, Angela M. Ribeiro, Lara Puetz, Jon Fjeldså, Robb T. Brumfield, Les Christidis, Mads Bertelsen, Dieter Thomas Tietze, Bruce C. Robertson, Gang Song, Gerald Borgia, Santiago Claramunt, Irby J. Lovette, Saul J. Cowen, Peter Njoroge, John Philip Dumbacher, Oliver A. Ryder, Jérôme Fuchs, Michael Bunce, David W. Burt, Joel Cracraft, Guanliang Meng, Shannon J. Hacketta, John Klickab, Peter G. Ryan, Knud Andreas Jønsson, Ian G. Jamieson, Rute R. da Fonseca, Edward Braun, Peter Houde, Siavash Mirarab, Alexander Suh, Martin Stervander, Paul B. Frandsen, Bengt Hansson, Hanna Sigeman, Suvi Ponnikas, Henriette Van der Zwan, Christopher N. Balakrishnan, Andrew G. Clark, John W. Fitzpatrick, Reed Bowman, Nancy Chen, Alison Cloutier, Timothy B. Sackton, Dustin J. Foote, Subir B. Shakya, Alain Vignal, André E. R. Soares, Beth Shapiro, Jacob González-Solís, Joan Ferrer-Obiol, Julio Rozas, Marta Riutort, Anna Tigano, Vicki Friesen, Love Dalén, Araxi O. Urrutia, Tamás Székely, Yang Liu, Michael G. Campana, Robert C. Fleischer, Kim Matthew Rutherford, Neil J. Gemmell, Nicolas Dussex, Henrik Mouritsen, Nadine Thiele, Kira Delmore, Miriam Liedvogel, Andre Franke, Marc P. Hoeppner, Oliver Krone, Adam M. Fudickar, Borja Milá, Ellen D. Ketterson, Andrew Eric Fidler, Guillermo Friis, Ángela María Parody-Merino, Phil F. Battley, Murray P. Cox, Nicholas Costa Barroso Lima, Francisco Prosdocimi, Thomas Lee Parchman, Barney A. Schlinger, Bette A. Loiselle, John G. Blake, Lainy B. Day, Matthew J. Fuxjager, Maude W. Baldwin, Michael J. Braun, Morgan Wirthlin, Rebecca B. Dikow, Thomas Brandt Ryder, Glauco Camenisch, Lukas F. Keller, Jeffrey M. DaCosta, Mark E. Hauber, Matthew I. M. Louder, Christopher C. Witt, Jimmy A. McGuire, Joann Mudge, Libby C. Megna, Matthew D. Carling, Biao Wang, Scott A. Taylor, Glaucia Del-Rio, Alexandre Aleixo, Ana Tereza Vasconcelos, Claudio V. Mello, Jason T. Weir, David Haussler, Qiye Li, Huanming Yang, Jiang Wang, Fumin Lei, Carsten Rahbek, Erich D. Jarvis, M. Thomas P. Gilbert, Gary R. Graves, Benedict Paten, and Guojie Zhang.
Many researchers are part of the 200 Mammals consortium. We thank the entire consortium, which includes but is not limited to: Diane P. Genereux, Jeremy Johnson, Voichita D. Marinescu, Eva Murén, Joel Armstrong, Aitor Serres, David deJuan, Gill Bejerano, Nicholas Casewell, Leona G. Chemnick, Joana Damas, Federica Di Palma, Mark Diekhans, Ian T. Fiddes, Manuel Garber, Linda Goodman, Wilfried Haerty, Maryls Houk, Robert Hubley, Teemu Kivioja, Lukas Kuderna, Eric S. Lander, Tomas Marques-Bonet, Jennifer RS. Meadows, William J. Murphy, Will Nash, Hyun Ji Noh, Martin Nweeia, Benedict Paten, Andreas R. Pfenning, Katie Pollard, David Ray, Beth Shapiro, Arian Smit, Mark Springer, Cynthia Steiner, Ross Swofford, Jussi Taipale, Emma C. Teeling, Jason Turner-Maier, Harris Lewin, Jessica Alfoldi, Oliver A. Ryder, Bruce Birren, Kerstin Lindblad-Toh, and Elinor K. Karlsson.
Please contact Joel Armstrong or Benedict Paten with questions about the hub. For questions specificially about the Bird 10K data, please contact the hub authors as well as Guojie Zhang. For questions about the 200 Mammals data, please contact the hub authors and Elinor Karlsson.