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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Phylogenomic analyses data of the avian phylogenomics project</title><author><name sortKey="Jarvis, Erich D" sort="Jarvis, Erich D" uniqKey="Jarvis E" first="Erich D" last="Jarvis">Erich D. Jarvis</name><affiliation><nlm:aff id="Aff1">Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC 27710 USA</nlm:aff></affiliation></author><author><name sortKey="Mirarab, Siavash" sort="Mirarab, Siavash" uniqKey="Mirarab S" first="Siavash" last="Mirarab">Siavash Mirarab</name><affiliation><nlm:aff id="Aff2">Department of Computer Science, The University of Texas at Austin, Austin, TX 78712 USA</nlm:aff></affiliation></author><author><name sortKey="Aberer, Andre J" sort="Aberer, Andre J" uniqKey="Aberer A" first="Andre J" last="Aberer">Andre J. Aberer</name><affiliation><nlm:aff id="Aff3">Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany</nlm:aff></affiliation></author><author><name sortKey="Li, Bo" sort="Li, Bo" uniqKey="Li B" first="Bo" last="Li">Bo Li</name><affiliation><nlm:aff id="Aff4">China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff></affiliation><affiliation><nlm:aff id="Aff5">College of Medicine and Forensics, Xi’an Jiaotong University, Xi’an, 710061 China</nlm:aff></affiliation><affiliation><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff></affiliation></author><author><name sortKey="Houde, Peter" sort="Houde, Peter" uniqKey="Houde P" first="Peter" last="Houde">Peter Houde</name><affiliation><nlm:aff id="Aff7">Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA</nlm:aff></affiliation></author><author><name sortKey="Li, Cai" sort="Li, Cai" uniqKey="Li C" first="Cai" last="Li">Cai Li</name><affiliation><nlm:aff id="Aff4">China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff></affiliation><affiliation><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff></affiliation></author><author><name sortKey="Ho, Simon Y W" sort="Ho, Simon Y W" uniqKey="Ho S" first="Simon Y W" last="Ho">Simon Y W. Ho</name><affiliation><nlm:aff id="Aff8">School of Biological Sciences, University of Sydney, Sydney, NSW 2006 Australia</nlm:aff></affiliation></author><author><name sortKey="Faircloth, Brant C" sort="Faircloth, Brant C" uniqKey="Faircloth B" first="Brant C" last="Faircloth">Brant C. Faircloth</name><affiliation><nlm:aff id="Aff9">Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095 USA</nlm:aff></affiliation><affiliation><nlm:aff id="Aff10">Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA</nlm:aff></affiliation></author><author><name sortKey="Nabholz, Benoit" sort="Nabholz, Benoit" uniqKey="Nabholz B" first="Benoit" last="Nabholz">Benoit Nabholz</name><affiliation><nlm:aff id="Aff11">CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Université Montpellier II, Montpellier, France</nlm:aff></affiliation></author><author><name sortKey="Howard, Jason T" sort="Howard, Jason T" uniqKey="Howard J" first="Jason T" last="Howard">Jason T. Howard</name><affiliation><nlm:aff id="Aff1">Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC 27710 USA</nlm:aff></affiliation></author><author><name sortKey="Suh, Alexander" sort="Suh, Alexander" uniqKey="Suh A" first="Alexander" last="Suh">Alexander Suh</name><affiliation><nlm:aff id="Aff12">Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden</nlm:aff></affiliation></author><author><name sortKey="Weber, Claudia C" sort="Weber, Claudia C" uniqKey="Weber C" first="Claudia C" last="Weber">Claudia C. Weber</name><affiliation><nlm:aff id="Aff12">Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden</nlm:aff></affiliation></author><author><name sortKey="Da Fonseca, Rute R" sort="Da Fonseca, Rute R" uniqKey="Da Fonseca R" first="Rute R" last="Da Fonseca">Rute R. Da Fonseca</name><affiliation><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff></affiliation></author><author><name sortKey="Alfaro Nu Ez, Alonzo" sort="Alfaro Nu Ez, Alonzo" uniqKey="Alfaro Nu Ez A" first="Alonzo" last="Alfaro-Nú Ez">Alonzo Alfaro-Nú Ez</name><affiliation><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff></affiliation></author><author><name sortKey="Narula, Nitish" sort="Narula, Nitish" uniqKey="Narula N" first="Nitish" last="Narula">Nitish Narula</name><affiliation><nlm:aff id="Aff7">Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA</nlm:aff></affiliation><affiliation><nlm:aff id="Aff13">Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa, 904-0495 Japan</nlm:aff></affiliation></author><author><name sortKey="Liu, Liang" sort="Liu, Liang" uniqKey="Liu L" first="Liang" last="Liu">Liang Liu</name><affiliation><nlm:aff id="Aff14">Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, 30602 USA</nlm:aff></affiliation></author><author><name sortKey="Burt, Dave" sort="Burt, Dave" uniqKey="Burt D" first="Dave" last="Burt">Dave Burt</name><affiliation><nlm:aff id="Aff15">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</nlm:aff></affiliation></author><author><name sortKey="Ellegren, Hans" sort="Ellegren, Hans" uniqKey="Ellegren H" first="Hans" last="Ellegren">Hans Ellegren</name><affiliation><nlm:aff id="Aff12">Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden</nlm:aff></affiliation></author><author><name sortKey="Edwards, Scott V" sort="Edwards, Scott V" uniqKey="Edwards S" first="Scott V" last="Edwards">Scott V. Edwards</name><affiliation><nlm:aff id="Aff16">Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA USA</nlm:aff></affiliation></author><author><name sortKey="Stamatakis, Alexandros" sort="Stamatakis, Alexandros" uniqKey="Stamatakis A" first="Alexandros" last="Stamatakis">Alexandros Stamatakis</name><affiliation><nlm:aff id="Aff3">Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany</nlm:aff></affiliation><affiliation><nlm:aff id="Aff17">Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany</nlm:aff></affiliation></author><author><name sortKey="Mindell, David P" sort="Mindell, David P" uniqKey="Mindell D" first="David P" last="Mindell">David P. Mindell</name><affiliation><nlm:aff id="Aff18">Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158 USA</nlm:aff></affiliation></author><author><name sortKey="Cracraft, Joel" sort="Cracraft, Joel" uniqKey="Cracraft J" first="Joel" last="Cracraft">Joel Cracraft</name><affiliation><nlm:aff id="Aff19">Department of Ornithology, American Museum of Natural History, New York, NY 10024 USA</nlm:aff></affiliation></author><author><name sortKey="Braun, Edward L" sort="Braun, Edward L" uniqKey="Braun E" first="Edward L" last="Braun">Edward L. Braun</name><affiliation><nlm:aff id="Aff20">Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611 USA</nlm:aff></affiliation></author><author><name sortKey="Warnow, Tandy" sort="Warnow, Tandy" uniqKey="Warnow T" first="Tandy" last="Warnow">Tandy Warnow</name><affiliation><nlm:aff id="Aff2">Department of Computer Science, The University of Texas at Austin, Austin, TX 78712 USA</nlm:aff></affiliation></author><author><name sortKey="Jun, Wang" sort="Jun, Wang" uniqKey="Jun W" first="Wang" last="Jun">Wang Jun</name><affiliation><nlm:aff id="Aff4">China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff></affiliation><affiliation><nlm:aff id="Aff21">Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark</nlm:aff></affiliation><affiliation><nlm:aff id="Aff22">Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia</nlm:aff></affiliation><affiliation><nlm:aff id="Aff23">Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, 999078 China</nlm:aff></affiliation><affiliation><nlm:aff id="Aff24">Department of Medicine, University of Hong Kong, Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Gilbert, M Thomas Pius" sort="Gilbert, M Thomas Pius" uniqKey="Gilbert M" first="M Thomas Pius" last="Gilbert">M Thomas Pius Gilbert</name><affiliation><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff></affiliation><affiliation><nlm:aff id="Aff25">Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, WA 6102 Australia</nlm:aff></affiliation></author><author><name sortKey="Zhang, Guojie" sort="Zhang, Guojie" uniqKey="Zhang G" first="Guojie" last="Zhang">Guojie Zhang</name><affiliation><nlm:aff id="Aff4">China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff></affiliation><affiliation><nlm:aff id="Aff26">Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25741440</idno><idno type="pmc">4349222</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4349222</idno><idno type="RBID">PMC:4349222</idno><idno type="doi">10.1186/s13742-014-0038-1</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000D19</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000D19</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Phylogenomic analyses data of the avian phylogenomics project</title><author><name sortKey="Jarvis, Erich D" sort="Jarvis, Erich D" uniqKey="Jarvis E" first="Erich D" last="Jarvis">Erich D. Jarvis</name><affiliation><nlm:aff id="Aff1">Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC 27710 USA</nlm:aff></affiliation></author><author><name sortKey="Mirarab, Siavash" sort="Mirarab, Siavash" uniqKey="Mirarab S" first="Siavash" last="Mirarab">Siavash Mirarab</name><affiliation><nlm:aff id="Aff2">Department of Computer Science, The University of Texas at Austin, Austin, TX 78712 USA</nlm:aff></affiliation></author><author><name sortKey="Aberer, Andre J" sort="Aberer, Andre J" uniqKey="Aberer A" first="Andre J" last="Aberer">Andre J. Aberer</name><affiliation><nlm:aff id="Aff3">Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany</nlm:aff></affiliation></author><author><name sortKey="Li, Bo" sort="Li, Bo" uniqKey="Li B" first="Bo" last="Li">Bo Li</name><affiliation><nlm:aff id="Aff4">China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff></affiliation><affiliation><nlm:aff id="Aff5">College of Medicine and Forensics, Xi’an Jiaotong University, Xi’an, 710061 China</nlm:aff></affiliation><affiliation><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff></affiliation></author><author><name sortKey="Houde, Peter" sort="Houde, Peter" uniqKey="Houde P" first="Peter" last="Houde">Peter Houde</name><affiliation><nlm:aff id="Aff7">Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA</nlm:aff></affiliation></author><author><name sortKey="Li, Cai" sort="Li, Cai" uniqKey="Li C" first="Cai" last="Li">Cai Li</name><affiliation><nlm:aff id="Aff4">China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff></affiliation><affiliation><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff></affiliation></author><author><name sortKey="Ho, Simon Y W" sort="Ho, Simon Y W" uniqKey="Ho S" first="Simon Y W" last="Ho">Simon Y W. Ho</name><affiliation><nlm:aff id="Aff8">School of Biological Sciences, University of Sydney, Sydney, NSW 2006 Australia</nlm:aff></affiliation></author><author><name sortKey="Faircloth, Brant C" sort="Faircloth, Brant C" uniqKey="Faircloth B" first="Brant C" last="Faircloth">Brant C. Faircloth</name><affiliation><nlm:aff id="Aff9">Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095 USA</nlm:aff></affiliation><affiliation><nlm:aff id="Aff10">Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA</nlm:aff></affiliation></author><author><name sortKey="Nabholz, Benoit" sort="Nabholz, Benoit" uniqKey="Nabholz B" first="Benoit" last="Nabholz">Benoit Nabholz</name><affiliation><nlm:aff id="Aff11">CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Université Montpellier II, Montpellier, France</nlm:aff></affiliation></author><author><name sortKey="Howard, Jason T" sort="Howard, Jason T" uniqKey="Howard J" first="Jason T" last="Howard">Jason T. Howard</name><affiliation><nlm:aff id="Aff1">Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC 27710 USA</nlm:aff></affiliation></author><author><name sortKey="Suh, Alexander" sort="Suh, Alexander" uniqKey="Suh A" first="Alexander" last="Suh">Alexander Suh</name><affiliation><nlm:aff id="Aff12">Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden</nlm:aff></affiliation></author><author><name sortKey="Weber, Claudia C" sort="Weber, Claudia C" uniqKey="Weber C" first="Claudia C" last="Weber">Claudia C. Weber</name><affiliation><nlm:aff id="Aff12">Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden</nlm:aff></affiliation></author><author><name sortKey="Da Fonseca, Rute R" sort="Da Fonseca, Rute R" uniqKey="Da Fonseca R" first="Rute R" last="Da Fonseca">Rute R. Da Fonseca</name><affiliation><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff></affiliation></author><author><name sortKey="Alfaro Nu Ez, Alonzo" sort="Alfaro Nu Ez, Alonzo" uniqKey="Alfaro Nu Ez A" first="Alonzo" last="Alfaro-Nú Ez">Alonzo Alfaro-Nú Ez</name><affiliation><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff></affiliation></author><author><name sortKey="Narula, Nitish" sort="Narula, Nitish" uniqKey="Narula N" first="Nitish" last="Narula">Nitish Narula</name><affiliation><nlm:aff id="Aff7">Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA</nlm:aff></affiliation><affiliation><nlm:aff id="Aff13">Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa, 904-0495 Japan</nlm:aff></affiliation></author><author><name sortKey="Liu, Liang" sort="Liu, Liang" uniqKey="Liu L" first="Liang" last="Liu">Liang Liu</name><affiliation><nlm:aff id="Aff14">Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, 30602 USA</nlm:aff></affiliation></author><author><name sortKey="Burt, Dave" sort="Burt, Dave" uniqKey="Burt D" first="Dave" last="Burt">Dave Burt</name><affiliation><nlm:aff id="Aff15">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</nlm:aff></affiliation></author><author><name sortKey="Ellegren, Hans" sort="Ellegren, Hans" uniqKey="Ellegren H" first="Hans" last="Ellegren">Hans Ellegren</name><affiliation><nlm:aff id="Aff12">Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden</nlm:aff></affiliation></author><author><name sortKey="Edwards, Scott V" sort="Edwards, Scott V" uniqKey="Edwards S" first="Scott V" last="Edwards">Scott V. Edwards</name><affiliation><nlm:aff id="Aff16">Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA USA</nlm:aff></affiliation></author><author><name sortKey="Stamatakis, Alexandros" sort="Stamatakis, Alexandros" uniqKey="Stamatakis A" first="Alexandros" last="Stamatakis">Alexandros Stamatakis</name><affiliation><nlm:aff id="Aff3">Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany</nlm:aff></affiliation><affiliation><nlm:aff id="Aff17">Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany</nlm:aff></affiliation></author><author><name sortKey="Mindell, David P" sort="Mindell, David P" uniqKey="Mindell D" first="David P" last="Mindell">David P. Mindell</name><affiliation><nlm:aff id="Aff18">Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158 USA</nlm:aff></affiliation></author><author><name sortKey="Cracraft, Joel" sort="Cracraft, Joel" uniqKey="Cracraft J" first="Joel" last="Cracraft">Joel Cracraft</name><affiliation><nlm:aff id="Aff19">Department of Ornithology, American Museum of Natural History, New York, NY 10024 USA</nlm:aff></affiliation></author><author><name sortKey="Braun, Edward L" sort="Braun, Edward L" uniqKey="Braun E" first="Edward L" last="Braun">Edward L. Braun</name><affiliation><nlm:aff id="Aff20">Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611 USA</nlm:aff></affiliation></author><author><name sortKey="Warnow, Tandy" sort="Warnow, Tandy" uniqKey="Warnow T" first="Tandy" last="Warnow">Tandy Warnow</name><affiliation><nlm:aff id="Aff2">Department of Computer Science, The University of Texas at Austin, Austin, TX 78712 USA</nlm:aff></affiliation></author><author><name sortKey="Jun, Wang" sort="Jun, Wang" uniqKey="Jun W" first="Wang" last="Jun">Wang Jun</name><affiliation><nlm:aff id="Aff4">China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff></affiliation><affiliation><nlm:aff id="Aff21">Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark</nlm:aff></affiliation><affiliation><nlm:aff id="Aff22">Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia</nlm:aff></affiliation><affiliation><nlm:aff id="Aff23">Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, 999078 China</nlm:aff></affiliation><affiliation><nlm:aff id="Aff24">Department of Medicine, University of Hong Kong, Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Gilbert, M Thomas Pius" sort="Gilbert, M Thomas Pius" uniqKey="Gilbert M" first="M Thomas Pius" last="Gilbert">M Thomas Pius Gilbert</name><affiliation><nlm:aff id="Aff6">Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</nlm:aff></affiliation><affiliation><nlm:aff id="Aff25">Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, WA 6102 Australia</nlm:aff></affiliation></author><author><name sortKey="Zhang, Guojie" sort="Zhang, Guojie" uniqKey="Zhang G" first="Guojie" last="Zhang">Guojie Zhang</name><affiliation><nlm:aff id="Aff4">China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</nlm:aff></affiliation><affiliation><nlm:aff id="Aff26">Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark</nlm:aff></affiliation></author></analytic><series><title level="j">GigaScience</title><idno type="eISSN">2047-217X</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses.</p></sec><sec><title>Findings</title><p>Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence.</p></sec><sec><title>Conclusions</title><p>The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13742-014-0038-1) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Jarvis, Ed" uniqKey="Jarvis E">ED Jarvis</name></author><author><name sortKey="Mirarab, S" uniqKey="Mirarab S">S Mirarab</name></author><author><name sortKey="Aberer, Aj" uniqKey="Aberer A">AJ Aberer</name></author><author><name sortKey="Li, B" uniqKey="Li B">B Li</name></author><author><name sortKey="Houde, P" uniqKey="Houde P">P Houde</name></author><author><name sortKey="Li, C" uniqKey="Li C">C Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, G" uniqKey="Zhang G">G Zhang</name></author><author><name sortKey="Li, C" uniqKey="Li C">C Li</name></author><author><name sortKey="Li, Q" uniqKey="Li Q">Q Li</name></author><author><name sortKey="Li, B" uniqKey="Li B">B Li</name></author><author><name sortKey="Larkin, Dm" uniqKey="Larkin D">DM Larkin</name></author><author><name sortKey="Lee, C" uniqKey="Lee C">C Lee</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Mirarab, S" uniqKey="Mirarab S">S Mirarab</name></author><author><name sortKey="Bayzid, Ms" uniqKey="Bayzid M">MS Bayzid</name></author><author><name sortKey="Boussau, B" uniqKey="Boussau B">B Boussau</name></author><author><name sortKey="Warnow, T" uniqKey="Warnow T">T Warnow</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Dickinson, Ec" uniqKey="Dickinson E">EC Dickinson</name></author><author><name sortKey="Remsen, Jv" uniqKey="Remsen J">JV Remsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gill, F" uniqKey="Gill F">F Gill</name></author><author><name sortKey="Wright, M" uniqKey="Wright M">M Wright</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hillier, Lw" uniqKey="Hillier L">LW Hillier</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author><author><name sortKey="Warren, W" uniqKey="Warren W">W Warren</name></author><author><name sortKey="Hardison, Rd" uniqKey="Hardison R">RD Hardison</name></author><author><name sortKey="Ponting, Cp" uniqKey="Ponting C">CP Ponting</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Warren, Wc" uniqKey="Warren W">WC Warren</name></author><author><name sortKey="Clayton, Df" uniqKey="Clayton D">DF Clayton</name></author><author><name sortKey="Ellegren, H" uniqKey="Ellegren H">H Ellegren</name></author><author><name sortKey="Arnold, Ap" uniqKey="Arnold A">AP Arnold</name></author><author><name sortKey="Hillier, Lw" uniqKey="Hillier L">LW Hillier</name></author><author><name sortKey="Kunstner, A" uniqKey="Kunstner A">A Künstner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Faircloth, Bc" uniqKey="Faircloth B">BC Faircloth</name></author><author><name sortKey="Mccormack, Je" uniqKey="Mccormack J">JE McCormack</name></author><author><name sortKey="Crawford, Ng" uniqKey="Crawford N">NG Crawford</name></author><author><name sortKey="Harvey, Mg" uniqKey="Harvey M">MG Harvey</name></author><author><name sortKey="Brumfield, Rt" uniqKey="Brumfield R">RT Brumfield</name></author><author><name sortKey="Glenn, Tc" uniqKey="Glenn T">TC Glenn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mccormack, Je" uniqKey="Mccormack J">JE McCormack</name></author><author><name sortKey="Faircloth, Bc" uniqKey="Faircloth B">BC Faircloth</name></author><author><name sortKey="Crawford, Ng" uniqKey="Crawford N">NG Crawford</name></author><author><name sortKey="Gowaty, Pa" uniqKey="Gowaty P">PA Gowaty</name></author><author><name sortKey="Brumfield, Rt" uniqKey="Brumfield R">RT Brumfield</name></author><author><name sortKey="Glenn, Tc" uniqKey="Glenn T">TC Glenn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dimitrieva, S" uniqKey="Dimitrieva S">S Dimitrieva</name></author><author><name sortKey="Bucher, P" uniqKey="Bucher P">P Bucher</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Harris, Rs" uniqKey="Harris R">RS Harris</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Blanchette, M" uniqKey="Blanchette M">M Blanchette</name></author><author><name sortKey="Faircloth, Bc" uniqKey="Faircloth B">BC Faircloth</name></author><author><name sortKey="Crawford, Ng" uniqKey="Crawford N">NG Crawford</name></author><author><name sortKey="Gowaty, Pa" uniqKey="Gowaty P">PA Gowaty</name></author><author><name sortKey="Brumfield, Rt" uniqKey="Brumfield R">RT Brumfield</name></author><author><name sortKey="Glenn, Tc" uniqKey="Glenn T">TC Glenn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simmons, Mp" uniqKey="Simmons M">MP Simmons</name></author><author><name sortKey="Ochoterena, H" uniqKey="Ochoterena H">H Ochoterena</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Young, Nd" uniqKey="Young N">ND Young</name></author><author><name sortKey="Healy, J" uniqKey="Healy J">J Healy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Katoh, K" uniqKey="Katoh K">K Katoh</name></author><author><name sortKey="Toh, H" uniqKey="Toh H">H Toh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Suh, A" uniqKey="Suh A">A Suh</name></author><author><name sortKey="Paus, M" uniqKey="Paus M">M Paus</name></author><author><name sortKey="Kiefmann, M" uniqKey="Kiefmann M">M Kiefmann</name></author><author><name sortKey="Churakov, G" uniqKey="Churakov G">G Churakov</name></author><author><name sortKey="Franke, Fa" uniqKey="Franke F">FA Franke</name></author><author><name sortKey="Brosius, J" uniqKey="Brosius J">J Brosius</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Suh, A" uniqKey="Suh A">A Suh</name></author><author><name sortKey="Kriegs, Jo" uniqKey="Kriegs J">JO Kriegs</name></author><author><name sortKey="Donnellan, S" uniqKey="Donnellan S">S Donnellan</name></author><author><name sortKey="Brosius, J" uniqKey="Brosius J">J Brosius</name></author><author><name sortKey="Schmitz, J" uniqKey="Schmitz J">J Schmitz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Suh, A" uniqKey="Suh A">A Suh</name></author><author><name sortKey="Churakov, G" uniqKey="Churakov G">G Churakov</name></author><author><name sortKey="Ramakodi, Mp" uniqKey="Ramakodi M">MP Ramakodi</name></author><author><name sortKey="Platt, Rn Nd" uniqKey="Platt R">RN 2nd Platt</name></author><author><name sortKey="Jurka, J" uniqKey="Jurka J">J Jurka</name></author><author><name sortKey="Kojima, Kk" uniqKey="Kojima K">KK Kojima</name></author><author><name sortKey="Caballero, J" uniqKey="Caballero J">J Caballero</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, K" uniqKey="Liu K">K Liu</name></author><author><name sortKey="Warnow, Tj" uniqKey="Warnow T">TJ Warnow</name></author><author><name sortKey="Holder, Mt" uniqKey="Holder M">MT Holder</name></author><author><name sortKey="Nelesen, Sm" uniqKey="Nelesen S">SM Nelesen</name></author><author><name sortKey="Yu, J" uniqKey="Yu J">J Yu</name></author><author><name sortKey="Stamatakis, Ap" uniqKey="Stamatakis A">AP Stamatakis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, K" uniqKey="Liu K">K Liu</name></author><author><name sortKey="Raghavan, S" uniqKey="Raghavan S">S Raghavan</name></author><author><name sortKey="Nelesen, S" uniqKey="Nelesen S">S Nelesen</name></author><author><name sortKey="Linder, Cr" uniqKey="Linder C">CR Linder</name></author><author><name sortKey="Warnow, T" uniqKey="Warnow T">T Warnow</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Loytynoja, A" uniqKey="Loytynoja A">A Löytynoja</name></author><author><name sortKey="Goldman, N" uniqKey="Goldman N">N Goldman</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Gigascience</journal-id><journal-id journal-id-type="iso-abbrev">Gigascience</journal-id><journal-title-group><journal-title>GigaScience</journal-title></journal-title-group><issn pub-type="epub">2047-217X</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25741440</article-id><article-id pub-id-type="pmc">4349222</article-id><article-id pub-id-type="publisher-id">38</article-id><article-id pub-id-type="doi">10.1186/s13742-014-0038-1</article-id><article-categories><subj-group subj-group-type="heading"><subject>Data Note</subject></subj-group></article-categories><title-group><article-title>Phylogenomic analyses data of the avian phylogenomics project</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes" equal-contrib="yes"><name><surname>Jarvis</surname><given-names>Erich D</given-names></name><address><email>jarvis@neuro.duke.edu</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Mirarab</surname><given-names>Siavash</given-names></name><address><email>smirarab@gmail.com</email></address><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author"><name><surname>Aberer</surname><given-names>Andre J</given-names></name><address><email>andre.aberer@gmail.com</email></address><xref ref-type="aff" rid="Aff3"></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Bo</given-names></name><address><email>libo@genomics.org.cn</email></address><xref ref-type="aff" rid="Aff4"></xref><xref ref-type="aff" rid="Aff5"></xref><xref ref-type="aff" rid="Aff6"></xref></contrib><contrib contrib-type="author"><name><surname>Houde</surname><given-names>Peter</given-names></name><address><email>phoude@nmsu.edu</email></address><xref ref-type="aff" rid="Aff7"></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Cai</given-names></name><address><email>licai@genomics.cn</email></address><xref ref-type="aff" rid="Aff4"></xref><xref ref-type="aff" rid="Aff6"></xref></contrib><contrib contrib-type="author"><name><surname>Ho</surname><given-names>Simon Y W</given-names></name><address><email>simon.ho@sydney.edu.au</email></address><xref ref-type="aff" rid="Aff8"></xref></contrib><contrib contrib-type="author"><name><surname>Faircloth</surname><given-names>Brant C</given-names></name><address><email>brant@faircloth-lab.org</email></address><xref ref-type="aff" rid="Aff9"></xref><xref ref-type="aff" rid="Aff10"></xref></contrib><contrib contrib-type="author"><name><surname>Nabholz</surname><given-names>Benoit</given-names></name><address><email>benoit.nabholz@gmail.com</email></address><xref ref-type="aff" rid="Aff11"></xref></contrib><contrib contrib-type="author"><name><surname>Howard</surname><given-names>Jason T</given-names></name><address><email>howard@neuro.duke.edu</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Suh</surname><given-names>Alexander</given-names></name><address><email>Alexander.Suh@ebc.uu.se</email></address><xref ref-type="aff" rid="Aff12"></xref></contrib><contrib contrib-type="author"><name><surname>Weber</surname><given-names>Claudia C</given-names></name><address><email>claudia.weber@ebc.uu.se</email></address><xref ref-type="aff" rid="Aff12"></xref></contrib><contrib contrib-type="author"><name><surname>da Fonseca</surname><given-names>Rute R</given-names></name><address><email>rute.r.da.fonseca@gmail.com</email></address><xref ref-type="aff" rid="Aff6"></xref></contrib><contrib contrib-type="author"><name><surname>Alfaro-Núñez</surname><given-names>Alonzo</given-names></name><address><email>alonzoalfaro@gmail.com</email></address><xref ref-type="aff" rid="Aff6"></xref></contrib><contrib contrib-type="author"><name><surname>Narula</surname><given-names>Nitish</given-names></name><address><email>nitishnarula19@gmail.com</email></address><xref ref-type="aff" rid="Aff7"></xref><xref ref-type="aff" rid="Aff13"></xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Liang</given-names></name><address><email>lliu@uga.edu</email></address><xref ref-type="aff" rid="Aff14"></xref></contrib><contrib contrib-type="author"><name><surname>Burt</surname><given-names>Dave</given-names></name><address><email>dave.burt@roslin.ed.ac.uk</email></address><xref ref-type="aff" rid="Aff15"></xref></contrib><contrib contrib-type="author"><name><surname>Ellegren</surname><given-names>Hans</given-names></name><address><email>Hans.Ellegren@ebc.uu.se</email></address><xref ref-type="aff" rid="Aff12"></xref></contrib><contrib contrib-type="author"><name><surname>Edwards</surname><given-names>Scott V</given-names></name><address><email>sedwards@fas.harvard.edu</email></address><xref ref-type="aff" rid="Aff16"></xref></contrib><contrib contrib-type="author"><name><surname>Stamatakis</surname><given-names>Alexandros</given-names></name><address><email>Alexandros.Stamatakis@h-its.org</email></address><xref ref-type="aff" rid="Aff3"></xref><xref ref-type="aff" rid="Aff17"></xref></contrib><contrib contrib-type="author"><name><surname>Mindell</surname><given-names>David P</given-names></name><address><email>dpmindell@gmail.com</email></address><xref ref-type="aff" rid="Aff18"></xref></contrib><contrib contrib-type="author"><name><surname>Cracraft</surname><given-names>Joel</given-names></name><address><email>jlc@amnh.org</email></address><xref ref-type="aff" rid="Aff19"></xref></contrib><contrib contrib-type="author"><name><surname>Braun</surname><given-names>Edward L</given-names></name><address><email>ebraun68@ufl.edu</email></address><xref ref-type="aff" rid="Aff20"></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Warnow</surname><given-names>Tandy</given-names></name><address><email>warnow@illinois.edu</email></address><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Jun</surname><given-names>Wang</given-names></name><address><email>wangj@genomics.org.cn</email></address><xref ref-type="aff" rid="Aff4"></xref><xref ref-type="aff" rid="Aff21"></xref><xref ref-type="aff" rid="Aff22"></xref><xref ref-type="aff" rid="Aff23"></xref><xref ref-type="aff" rid="Aff24"></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Gilbert</surname><given-names>M Thomas Pius</given-names></name><address><email>mtpgilbert@gmail.com</email></address><xref ref-type="aff" rid="Aff6"></xref><xref ref-type="aff" rid="Aff25"></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Zhang</surname><given-names>Guojie</given-names></name><address><email>zhanggj@genomics.cn</email></address><xref ref-type="aff" rid="Aff4"></xref><xref ref-type="aff" rid="Aff26"></xref></contrib><contrib contrib-type="author"><collab>The Avian Phylogenomics Consortium</collab></contrib><aff id="Aff1"><label></label>Department of Neurobiology, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC 27710 USA</aff><aff id="Aff2"><label></label>Department of Computer Science, The University of Texas at Austin, Austin, TX 78712 USA</aff><aff id="Aff3"><label></label>Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany</aff><aff id="Aff4"><label></label>China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China</aff><aff id="Aff5"><label></label>College of Medicine and Forensics, Xi’an Jiaotong University, Xi’an, 710061 China</aff><aff id="Aff6"><label></label>Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark</aff><aff id="Aff7"><label></label>Department of Biology, New Mexico State University, Las Cruces, NM 88003 USA</aff><aff id="Aff8"><label></label>School of Biological Sciences, University of Sydney, Sydney, NSW 2006 Australia</aff><aff id="Aff9"><label></label>Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095 USA</aff><aff id="Aff10"><label></label>Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA</aff><aff id="Aff11"><label></label>CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Université Montpellier II, Montpellier, France</aff><aff id="Aff12"><label></label>Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden</aff><aff id="Aff13"><label></label>Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa, 904-0495 Japan</aff><aff id="Aff14"><label></label>Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, 30602 USA</aff><aff id="Aff15"><label></label>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</aff><aff id="Aff16"><label></label>Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA USA</aff><aff id="Aff17"><label></label>Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany</aff><aff id="Aff18"><label></label>Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158 USA</aff><aff id="Aff19"><label></label>Department of Ornithology, American Museum of Natural History, New York, NY 10024 USA</aff><aff id="Aff20"><label></label>Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611 USA</aff><aff id="Aff21"><label></label>Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark</aff><aff id="Aff22"><label></label>Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia</aff><aff id="Aff23"><label></label>Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, 999078 China</aff><aff id="Aff24"><label></label>Department of Medicine, University of Hong Kong, Hong Kong, Hong Kong</aff><aff id="Aff25"><label></label>Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, WA 6102 Australia</aff><aff id="Aff26"><label></label>Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark</aff></contrib-group><pub-date pub-type="epub"><day>12</day><month>2</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>12</day><month>2</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>4</volume><elocation-id>4</elocation-id><history><date date-type="received"><day>26</day><month>11</month><year>2014</year></date><date date-type="accepted"><day>16</day><month>12</month><year>2014</year></date></history><permissions><copyright-statement>© Jarvis et al.; licensee BioMed Central. 2015</copyright-statement><license license-type="open-access"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p>Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses.</p></sec><sec><title>Findings</title><p>Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence.</p></sec><sec><title>Conclusions</title><p>The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13742-014-0038-1) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>Avian genomes</kwd><kwd>Phylogenomics</kwd><kwd>Sequence alignments</kwd><kwd>Species tree</kwd><kwd>Gene trees</kwd><kwd>Indels</kwd><kwd>Transposable elements</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2015</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="Sec1"><title>Data description</title><p>Here we present FASTA files of loci, sequence alignments, indels, transposable elements, and Newick files of gene trees and species trees used in the Avian Phylogenomics Project [<xref ref-type="bibr" rid="CR1">1</xref>-<xref ref-type="bibr" rid="CR4">4</xref>]. We also include scripts used to process the data. The 48 species from which we collected these data span the phylogeny of modern birds, including representatives of all Neognathae (Neoaves and Galloanseres) and two of the five Palaeognathae orders (Table <xref rid="Tab1" ref-type="table">1</xref>) [<xref ref-type="bibr" rid="CR5">5</xref>-<xref ref-type="bibr" rid="CR7">7</xref>].<table-wrap id="Tab1"><label>Table 1</label><caption><p><bold>Genomes used in the avian phylogenomics project</bold></p></caption><table frame="hsides" rules="groups"><thead><tr valign="top"><th><bold>Species</bold></th><th><bold>English name</bold></th><th><bold>BioProject ID</bold></th><th><bold>GigaScience</bold></th></tr></thead><tbody><tr valign="top"><td><italic>Acanthisitta chloris</italic></td><td>Rifleman</td><td>PRJNA212877</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101015">http://dx.doi.org/10.5524/101015</ext-link></td></tr><tr valign="top"><td><italic>Anas platyrhynchos</italic></td><td>Pekin Duck</td><td>PRJNA46621</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101001">http://dx.doi.org/10.5524/101001</ext-link></td></tr><tr valign="top"><td><italic>Antrostomus carolinensis</italic></td><td>Chuck-will’s-widow</td><td>PRJNA212888</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101019">http://dx.doi.org/10.5524/101019</ext-link></td></tr><tr valign="top"><td><italic>Apaloderma vittatum</italic></td><td>Bar-tailed Trogon</td><td>PRJNA212878</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101016">http://dx.doi.org/10.5524/101016</ext-link></td></tr><tr valign="top"><td><italic>Aptenodytes forsteri</italic></td><td>Emperor Penguin</td><td>PRJNA235982</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/100005">http://dx.doi.org/10.5524/100005</ext-link></td></tr><tr valign="top"><td><italic>Balearica regulorum</italic></td><td>Grey Crowned-crane</td><td>PRJNA212879</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101017">http://dx.doi.org/10.5524/101017</ext-link></td></tr><tr valign="top"><td><italic>Buceros rhinoceros</italic></td><td>Rhinoceros Hornbill</td><td>PRJNA212887</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101018">http://dx.doi.org/10.5524/101018</ext-link></td></tr><tr valign="top"><td><italic>Calypte anna</italic></td><td>Anna’s Hummingbird</td><td>PRJNA212866</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101004">http://dx.doi.org/10.5524/101004</ext-link></td></tr><tr valign="top"><td><italic>Cariama cristata</italic></td><td>Red-legged Seriema</td><td>PRJNA212889</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101020">http://dx.doi.org/10.5524/101020</ext-link></td></tr><tr valign="top"><td><italic>Cathartes aura</italic></td><td>Turkey Vulture</td><td>PRJNA212890</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101021">http://dx.doi.org/10.5524/101021</ext-link></td></tr><tr valign="top"><td><italic>Chaetura pelagica</italic></td><td>Chimney Swift</td><td>PRJNA210808</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101005">http://dx.doi.org/10.5524/101005</ext-link></td></tr><tr valign="top"><td><italic>Charadrius vociferus</italic></td><td>Killdeer</td><td>PRJNA212867</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101007">http://dx.doi.org/10.5524/101007</ext-link></td></tr><tr valign="top"><td><italic>Chlamydotis macqueenii</italic></td><td>MacQueen’s Bustard</td><td>PRJNA212891</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101022">http://dx.doi.org/10.5524/101022</ext-link></td></tr><tr valign="top"><td><italic>Colius striatus</italic></td><td>Speckled Mousebird</td><td>PRJNA212892</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101023">http://dx.doi.org/10.5524/101023</ext-link></td></tr><tr valign="top"><td><italic>Columba livia</italic></td><td>Pigeon</td><td>PRJNA167554</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/100007">http://dx.doi.org/10.5524/100007</ext-link></td></tr><tr valign="top"><td><italic>Corvus brachyrhynchos</italic></td><td>American Crow</td><td>PRJNA212869</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101008">http://dx.doi.org/10.5524/101008</ext-link></td></tr><tr valign="top"><td><italic>Cuculus canorus</italic></td><td>Common Cuckoo</td><td>PRJNA212870</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101009">http://dx.doi.org/10.5524/101009</ext-link></td></tr><tr valign="top"><td><italic>Egretta garzetta</italic></td><td>Little Egret</td><td>PRJNA232959</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101002">http://dx.doi.org/10.5524/101002</ext-link></td></tr><tr valign="top"><td><italic>Eurypyga helias</italic></td><td>Sunbittern</td><td>PRJNA212893</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101024">http://dx.doi.org/10.5524/101024</ext-link></td></tr><tr valign="top"><td><italic>Falco peregrinus</italic></td><td>Peregrine Falcon</td><td>PRJNA159791</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101006">http://dx.doi.org/10.5524/101006</ext-link></td></tr><tr valign="top"><td><italic>Fulmarus glacialis</italic></td><td>Northern Fulmar</td><td>PRJNA212894</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101025">http://dx.doi.org/10.5524/101025</ext-link></td></tr><tr valign="top"><td><italic>Gallus gallus</italic></td><td>Chicken</td><td>PRJNA13342</td><td>N.A.</td></tr><tr valign="top"><td><italic>Gavia stellata</italic></td><td>Red-throated Loon</td><td>PRJNA212895</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101026">http://dx.doi.org/10.5524/101026</ext-link></td></tr><tr valign="top"><td><italic>Geospiza fortis</italic></td><td>Medium Ground-finch</td><td>PRJNA156703</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/100040">http://dx.doi.org/10.5524/100040</ext-link></td></tr><tr valign="top"><td><italic>Haliaeetus albicilla</italic></td><td>White-tailed Eagle</td><td>PRJNA212896</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101027">http://dx.doi.org/10.5524/101027</ext-link></td></tr><tr valign="top"><td><italic>Haliaeetus leucocephalus</italic></td><td>Bald Eagle</td><td>PRJNA237821</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101040">http://dx.doi.org/10.5524/101040</ext-link></td></tr><tr valign="top"><td><italic>Leptosomus discolor</italic></td><td>Cuckoo-roller</td><td>PRJNA212897</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101028">http://dx.doi.org/10.5524/101028</ext-link></td></tr><tr valign="top"><td><italic>Manacus vitellinus</italic></td><td>Golden-collared Manakin</td><td>PRJNA212872</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101010">http://dx.doi.org/10.5524/101010</ext-link></td></tr><tr valign="top"><td><italic>Meleagris gallopavo</italic></td><td>Turkey</td><td>PRJNA42129</td><td>N.A.</td></tr><tr valign="top"><td><italic>Melopsittacus undulatus</italic></td><td>Budgerigar</td><td>PRJNA72527</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/100059">http://dx.doi.org/10.5524/100059</ext-link></td></tr><tr valign="top"><td><italic>Merops nubicus</italic></td><td>Carmine Bee-eater</td><td>PRJNA212898</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101029">http://dx.doi.org/10.5524/101029</ext-link></td></tr><tr valign="top"><td><italic>Mesitornis unicolor</italic></td><td>Brown Mesite</td><td>PRJNA212899</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101030">http://dx.doi.org/10.5524/101030</ext-link></td></tr><tr valign="top"><td><italic>Nestor notabilis</italic></td><td>Kea</td><td>PRJNA212900</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101031">http://dx.doi.org/10.5524/101031</ext-link></td></tr><tr valign="top"><td><italic>Nipponia nippon</italic></td><td>Crested ibis</td><td>PRJNA232572</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101003">http://dx.doi.org/10.5524/101003</ext-link></td></tr><tr valign="top"><td><italic>Opisthocomus hoazin</italic></td><td>Hoatzin</td><td>PRJNA212873</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101011">http://dx.doi.org/10.5524/101011</ext-link></td></tr><tr valign="top"><td><italic>Pelecanus crispus</italic></td><td>Dalmatian Pelican</td><td>PRJNA212901</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101032">http://dx.doi.org/10.5524/101032</ext-link></td></tr><tr valign="top"><td><italic>Phaethon lepturus</italic></td><td>White-tailed Tropicbird</td><td>PRJNA212902</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101033">http://dx.doi.org/10.5524/101033</ext-link></td></tr><tr valign="top"><td><italic>Phalacrocorax carbo</italic></td><td>Great Cormorant</td><td>PRJNA212903</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101034">http://dx.doi.org/10.5524/101034</ext-link></td></tr><tr valign="top"><td><italic>Phoenicopterus ruber</italic></td><td>American Flamingo</td><td>PRJNA212904</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101035">http://dx.doi.org/10.5524/101035</ext-link></td></tr><tr valign="top"><td><italic>Picoides pubescens</italic></td><td>Downy Woodpecker</td><td>PRJNA212874</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101012">http://dx.doi.org/10.5524/101012</ext-link></td></tr><tr valign="top"><td><italic>Podiceps cristatus</italic></td><td>Great Crested Grebe</td><td>PRJNA212905</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101036">http://dx.doi.org/10.5524/101036</ext-link></td></tr><tr valign="top"><td><italic>Pterocles gutturalis</italic></td><td>Yellow-throated Sandgrouse</td><td>PRJNA212906</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101037">http://dx.doi.org/10.5524/101037</ext-link></td></tr><tr valign="top"><td><italic>Pygoscelis adeliae</italic></td><td>Adelie Penguin</td><td>PRJNA235983</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/100006">http://dx.doi.org/10.5524/100006</ext-link></td></tr><tr valign="top"><td><italic>Struthio camelus</italic></td><td>Common Ostrich</td><td>PRJNA212875</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101013">http://dx.doi.org/10.5524/101013</ext-link></td></tr><tr valign="top"><td><italic>Taeniopygia guttata</italic></td><td>Zebra Finch</td><td>PRJNA17289</td><td>N.A.</td></tr><tr valign="top"><td><italic>Tauraco erythrolophus</italic></td><td>Red-crested Turaco</td><td>PRJNA212908</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101038">http://dx.doi.org/10.5524/101038</ext-link></td></tr><tr valign="top"><td><italic>Tinamus guttatus</italic></td><td>White-throated Tinamou</td><td>PRJNA212876</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101014">http://dx.doi.org/10.5524/101014</ext-link></td></tr><tr valign="top"><td><italic>Tyto alba</italic></td><td>Barn Owl</td><td>PRJNA212909</td><td><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101039">http://dx.doi.org/10.5524/101039</ext-link></td></tr></tbody></table><table-wrap-foot><p>Listed are the scientific species name, English name, BioProject ID in the NCBI database for each genome (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/bioproject">http://www.ncbi.nlm.nih.gov/bioproject</ext-link>), and <italic>GigaScience</italic> deposited genome sequences and raw reads. Full details are in [<xref ref-type="bibr" rid="CR1">1</xref>,<xref ref-type="bibr" rid="CR2">2</xref>].</p></table-wrap-foot></table-wrap></p><sec id="Sec2"><title>Explanation of various data sets used to infer gene and species trees</title><p>Here we describe each locus data set in brief. Additional details are provided in Jarvis et al. [<xref ref-type="bibr" rid="CR1">1</xref>].</p><sec id="Sec3"><title>8295 protein-coding exon gene set</title><p>This is an exon-coding sequence data set of 8295 genes based on synteny-defined orthologs we identified and selected from the assembled genomes of chicken and zebra finch [<xref ref-type="bibr" rid="CR8">8</xref>,<xref ref-type="bibr" rid="CR9">9</xref>]. We required these loci to be present in at least 42 of the 48 avian species and outgroups, which allowed for missing data due to incomplete assemblies. To be included in the dataset, the exons in each genome assembly had to be 30% or more of the full-length sequence of the chicken or zebra finch ortholog. Annotated untranslated regions (UTRs) were trimmed off to remove non-coding sequence, in order to infer a coding-only sequence phylogeny. We note that 44 genes were identified with various problems such as gene annotation issues, and we removed them in the phylogenetic analyses. However, we provide them here in the unfiltered alignments.</p></sec><sec id="Sec4"><title>8295 protein amino acid alignment set</title><p>These are alignments of the translated peptide sequences for the 8295 protein-coding gene data set.</p></sec><sec id="Sec5"><title>2516 intron gene set</title><p>This is an orthologous subset of introns from the 8295 protein-coding genes among 52 species (includes outgroups). Introns with conserved annotated exon-intron boundaries between chicken and another species (±1 codon) were chosen. We filtered out introns with length < 50 bp or intron length ratio > 1.5 between chicken and another species or another species and chicken. This filtering resulted in a conservative subset of introns that could be reliably identified and aligned.</p></sec><sec id="Sec6"><title>3679 UCE locus set</title><p>This is the ultraconserved element (UCE) data set with 1000 bp flanking sequence at the 3′ and 5′ ends. The UCE dataset was filtered to remove overlap with the above exon and intron data sets, other exons and introns in the chicken genome assembly version 3, and overlapping sequences among the UCEs. The source UCE sequences used to search the genomes were determined from sequence capture probes [<xref ref-type="bibr" rid="CR10">10</xref>-<xref ref-type="bibr" rid="CR12">12</xref>] aligned to each avian genome assembly. Unlike the exon and intron data sets, we required that all 42 avian species and the alligator outgroup contain the UCEs. We found this requirement to be sufficient, because the central portions of UCEs are highly conserved across all species.</p></sec><sec id="Sec7"><title>High and low variance introns and exons</title><p>These four data sets represent the 10% subsets of the 8295 exons and their associated introns when available (i.e. from the same genes) that had the highest and lowest variance in GC3 (third codon position) content across species. To calculate GC3 variance, we first calculated GC3 for each ortholog in each species, and then we used the correlation coefficient R to calculate variance in GC3 for each species. Orthologs were ranked by their GC3 variance and we selected the top and bottom 10% for analyses.</p></sec><sec id="Sec8"><title>Supergenes</title><p>These are the concatenated sets of loci from various partitions of the TENT dataset (exons, introns, and UCEs described above), brought together using the statistical binning approach. The statistical binning approach put together sets of loci that were deemed “combinable”. Two genes were considered combinable if their respective gene trees had no pairs of incompatible branches that had bootstrap support above a 50% threshold. Alignments of genes in the same bin were concatenated to form supergenes, but boundaries of genes were kept so that a gene-partitioned phylogenetic analysis could be performed on each supergene.</p></sec><sec id="Sec9"><title>Whole genome alignment</title><p>Whole genome alignments were first created by a LASTZ + MULTIZ alignment [<xref ref-type="bibr" rid="CR13">13</xref>,<xref ref-type="bibr" rid="CR14">14</xref>] (<ext-link ext-link-type="uri" xlink:href="http://www.bx.psu.edu/miller_lab/">http://www.bx.psu.edu/miller_lab/</ext-link>) across all 48 bird species and outgroups using individual chromosomes of the chicken genome as the reference (initial alignment 392,719,329 Mb). They were filtered for segments with fewer than 42 avian species (>5 missing bird species) and aberrant sequence alignments. The individual remaining segments of the MULTIZ alignment were realigned with MAFFT. We did not use SATé + MAFFT due to computational challenges (too much input/output was required).</p></sec><sec id="Sec10"><title>Indel dataset</title><p>5.7 million insertions and deletions (indels) were scored as binary characters locus by locus from the same intron, exon, and UCE alignments as used in the TENT data set on the principle of simple indel coding using 2Xread [<xref ref-type="bibr" rid="CR15">15</xref>,<xref ref-type="bibr" rid="CR16">16</xref>] and then concatenated. Coding was verified using GapCoder [<xref ref-type="bibr" rid="CR17">17</xref>] and by visual inspection of alignments for a small subset of data. Intron indels were scored on alignments that excluded non-avian outgroups (48 taxa), UCE indels were scored on alignments that included Alligator (49 taxa), and exons were scored on alignments that included all non-avian outgroups (52 taxa). Individual introns of the same gene were scored independently to avoid creating artifactual indels between concatenated intron or whole genome segments, whereas exons were concatenated as complete unigenes before scoring. For exons, indels >30 bp were excluded to avoid scoring missing exons as indels.</p></sec><sec id="Sec11"><title>Transposable element markers</title><p>These are 61 manually curated presence/absence loci of transposable elements (TEs) present in the Barn Owl genome that exhibit presence at orthologous positions in one or more of the other avian species. The TE markers were identified by eye after a computational screening of 3,671 TguLTR5d retroposon insertions from the Barn Owl. For each TguLTR5d locus, we conducted BLASTn searches of TE-flanking sequences (1 kb per flank) against the remaining avian species and generated multispecies sequence alignments using MAFFT [<xref ref-type="bibr" rid="CR18">18</xref>]. Redundant or potentially paralogous loci were excluded from analysis and the remaining marker candidates were carefully inspected using strict standard criteria for assigning presence/absence character states [<xref ref-type="bibr" rid="CR19">19</xref>-<xref ref-type="bibr" rid="CR21">21</xref>].</p></sec></sec><sec id="Sec12"><title>FASTA files of loci datasets in alignments</title><p>We provide the above loci data sets as FASTA files of both unfiltered and filtered sequence alignments. The alignments were filtered for aberrant over- and under-aligned sequences, and for the presence of the loci in 42 of the 48 avian species. All multiple sequence alignments were performed in two rounds. The first round was used to find contiguous portions of sequences that we identified as aberrant, and the second round was used to realign the filtered sequences. We used SATé [<xref ref-type="bibr" rid="CR22">22</xref>,<xref ref-type="bibr" rid="CR23">23</xref>] combined with either MAFFT [<xref ref-type="bibr" rid="CR18">18</xref>] or PRANK [<xref ref-type="bibr" rid="CR24">24</xref>] alignment algorithms, depending on the limitations of working with large datasets. Alignments without and with outgroups are made available.</p></sec><sec id="Sec13"><title>Filtered loci sequence alignments</title><sec id="Sec14"><title>Exon loci alignments</title><p>These are filtered alignments of exons from 8295 genes. Of these 8295, there were 42 genes that were identified to have annotation issues and we removed them from the phylogenetic analyses (the list is provided in the file FASTA_files_of_loci_datasets/Filtered_sequence_alignments/8295_Exons/42-exon-genes-removed.txt). Two more genes were removed because a gene tree could not be estimated for them. The first round of alignment was performed using SATé + PRANK, and the second round was performed using SATé + MAFFT. Before alignment, the nucleotide sequences were converted to amino acid sequences, and then reverted back to nucleotide sequences afterwards.</p><p>8295 Exons<list list-type="bullet"><list-item><p>42-exon-genes-removed.txt: list of 42 genes removed due to various issues</p></list-item><list-item><p>pep2cds-filtered-sate-alignments-noout.tar.gz: DNA alignments (Amino acid alignments translated to DNA) without outgroups</p></list-item><list-item><p>pep2cds-filtered-sate-alignments-original.zip: DNA alignments (Amino acid alignments translated to DNA) with outgroups included</p></list-item></list></p><p>8295 Amino Acids<list list-type="bullet"><list-item><p>pep-filtered-sate-alignments-noout.tar.gz: Amino acid alignments with outgroups removed</p></list-item><list-item><p>pep-filtered-sate-alignments-original.zip: Amino acid alignments with outgroups included</p></list-item></list></p></sec><sec id="Sec15"><title>Intron loci alignments</title><p>These are filtered alignments of introns from 2516 genes. Both rounds of alignment were performed using SATé + MAFFT, because SATé + PRANK was too computationally expensive on long introns.</p><p>2516 Introns<list list-type="bullet"><list-item><p>introns-filtered-sate-alignments-with-and-without-outgroups.tar.gz: Includes both alignments with and without outgroups</p></list-item></list></p></sec><sec id="Sec16"><title>UCE loci alignments</title><p>These are alignments of UCEs and their surrounding 1000 bp from 3769 loci after filtering. Both rounds of alignment were performed using SATé + MAFFT.</p><p>3769 UCE + 1000 flanking bp<list list-type="bullet"><list-item><p>uce-probes-used.fasta.gz: Probes targeting UCE loci shared among vertebrate taxa.</p></list-item><list-item><p>uce-raw-genome-slices-of-probe-matches.tar: Probe + flank slices around locations matching probes targeting UCE loci.</p></list-item><list-item><p>uce-raw-lastz-results-of-probe-matches.tar: LASTZ results of mapping probes onto genome assemblies.</p></list-item><list-item><p>uce-assembled-loci-from-probe-matches.tar: UCE loci assembled from probe + flank slices from each genome.</p></list-item><list-item><p>uce-filtered-alignments-w-gator.tar.gz: UCE individual alignments without outgroups</p></list-item><list-item><p>uce-filtered-alignments-without-gator.tar.gz: UCE individual alignments with outgroups</p></list-item></list></p></sec><sec id="Sec17"><title>Supergenes generated from statistical binning</title><p>These are concatenated alignments for each of our 2022 supergene alignments. We note that although supergenes are concatenated loci, we estimated supergene trees using partitioned analyses where each gene was put in a different partition. Thus, we also provide the boundaries between genes in text files (these can be directly used as partition input files to RAxML).<list list-type="bullet"><list-item><p>supergene-alignments.tar.bz2: supergene alignments with partition files showing genes put in each bin and their boundaries in the concatenated alignment</p></list-item></list></p></sec></sec><sec id="Sec18"><title>Unfiltered loci sequence alignments</title><p>These are individual loci alignments of the above data sets, before filtering.</p><p>Amino.Acid.unfiltered<list list-type="bullet"><list-item><p>pep-unfiltered-alignments-original.zip: unfiltered SATé + Prank alignments used for the filtering step</p></list-item></list></p><p>Exon.c123.unfiltered:<list list-type="bullet"><list-item><p>pep2cds-unfiltered-alignemtns-original.zip: unfiltered SATé + Prank alignments used for the filtering step</p></list-item></list></p><p>Intron.unfiltered<list list-type="bullet"><list-item><p>introns-unfiltered-alignments-original.zip: intron SATé alignments before filtering with outgroups included</p></list-item><list-item><p>introns-unfiltered-alignments-noout.zip: intron SATé alignments before filtering with outgroups included</p></list-item></list></p><p>UCE.unfiltered<list list-type="bullet"><list-item><p>uce-unfiltered-alignments-w-gator.tar.gz: UCE alignments before filtering with alligator outgroup</p></list-item></list></p><p>WGT.unfiltered<list list-type="bullet"><list-item><p>These are uploaded as part of the comparative genomics paper [<xref ref-type="bibr" rid="CR2">2</xref>] data note [<xref ref-type="bibr" rid="CR25">25</xref>], and a link is provided here <ext-link ext-link-type="uri" xlink:href="https://github.com/gigascience/paper-zhang2014">https://github.com/gigascience/paper-zhang2014</ext-link>.</p></list-item></list></p></sec><sec id="Sec19"><title>FASTA files of concatenated datasets in alignments</title><p>We provide FASTA files of concatenated sequence alignments of the above filtered loci datasets. These are concatenated alignments that were used in the ExaML and RAxML analyses [<xref ref-type="bibr" rid="CR3">3</xref>].</p><sec id="Sec20"><title>Concatenated alignments used in ExaML analyses</title><p><list list-type="bullet"><list-item><p>Exon.AminoAcid.ExaML.partitioned</p></list-item><list-item><p>Exon.c123. ExaML.partitioned</p></list-item><list-item><p>Exon.c123. ExaML.unpartitioned</p></list-item><list-item><p>Exon.c1.ExaML.unpartitioned</p></list-item><list-item><p>Exon.c2.ExaML.unpartitioned</p></list-item><list-item><p>Exon.c12.ExaML.unpartitioned</p></list-item><list-item><p>Exon.c123-RY.ExaML.unpartitioned</p></list-item><list-item><p>Exon.c3.ExaML.unpartitioned</p></list-item><list-item><p>Intron</p></list-item><list-item><p>TEIT.RAxML</p></list-item><list-item><p>TENT + c3.ExaML</p></list-item><list-item><p>TENT + outgroup.ExaML</p></list-item><list-item><p>TENT.ExaML.100%</p></list-item><list-item><p>TENT.ExaML.25%</p></list-item><list-item><p>TENT.ExaML.50%</p></list-item><list-item><p>TENT.ExaML.75%</p></list-item><list-item><p>WGT.ExaML</p></list-item></list></p></sec><sec id="Sec21"><title>Concatenated alignments used in RAxML analyses</title><p>UCE concatenated alignments with and without the alligator<list list-type="bullet"><list-item><p>uce-filtered-alignments-w-gator-concatenated.phylip.gz</p></list-item><list-item><p>uce-filtered-alignments-without-gator-concatenated.phylip.gz</p></list-item></list></p></sec><sec id="Sec22"><title>Clocklike exon alignment</title><p>Concatenated c12 (1st + 2nd codons) DNA sequence alignments from the 1156 clocklike genes were used for the dating analyses. These are alignments of the first and second codon positions of clock-like genes among the 8295 exon orthologs:<list list-type="bullet"><list-item><p>c12.DNA.alignment.1156.clocklike.zip</p></list-item><list-item><p>c12.DNA.alignment.1156.clocklike.txt</p></list-item><list-item><p>c12.DNA.alignment.clocklike.readme.txt</p></list-item><list-item><p>c12.DNA.alignment.clocklike.txt.zip</p></list-item></list></p></sec><sec id="Sec23"><title>High and low variance exons and their associated introns</title><p><list list-type="bullet"><list-item><p>High variance exons:</p></list-item></list><list list-type="bullet"><list-item><p>Exon.heterogeneous.c123</p></list-item><list-item><p>Exon.heterogenous.c12</p></list-item></list><list list-type="bullet"><list-item><p>Low variance exons:</p></list-item></list><list list-type="bullet"><list-item><p>Exon.homogeneous.c123.</p></list-item><list-item><p>Exon.homogenous.c12</p></list-item></list><list list-type="bullet"><list-item><p>High variance introns: These are heterogenous introns</p></list-item></list><list list-type="bullet"><list-item><p>concatIntronNooutMSAlow.fasta.gz</p></list-item></list><list list-type="bullet"><list-item><p>Low variance introns: These are homogenous introns</p></list-item></list><list list-type="bullet"><list-item><p>concatIntronNooutMSAhigh.fasta.gz</p></list-item></list></p></sec><sec id="Sec24"><title>Indel sequence alignments</title><p>This is a concatenated alignment of indels from exons, introns, and UCEs. A README file describes the content.</p></sec></sec><sec id="Sec25"><title>Transposable element markers</title><p><list list-type="bullet"><list-item><p>owl_TE_marker_Table.txt</p></list-item></list></p></sec><sec id="Sec26"><title>Species and gene tree files</title><p>Species trees (Newick format) were generated with either RAxML, an improved ExaML version for handling large alignments, or MP-EST* [<xref ref-type="bibr" rid="CR4">4</xref>]. We deposit both the maximum likelihood and bootstrap replicate trees.</p><sec id="Sec27"><title>Newick files for 32 species trees using different genomic partitions and methods</title><p><list list-type="bullet"><list-item><p>Exon.AminoAcid.ExaML.partitioned.tre</p></list-item><list-item><p>Exon.c123.ExaML.partitioned.tre</p></list-item><list-item><p>Exon.c123.ExaML.unpartititoned.tre</p></list-item><list-item><p>Exon.c123-RY.ExaML.unpartitioned.tre</p></list-item><list-item><p>Exon.c12.ExaML.partitioned.tre</p></list-item><list-item><p>Exon.c12.ExaML.unpartitioned.tre</p></list-item><list-item><p>Exon.c1.ExaML.unpartitioned.tre</p></list-item><list-item><p>Exon.c2.ExaML.unpartitioned.tre</p></list-item><list-item><p>Exon.c3.ExaML.unpartitioned.tre</p></list-item><list-item><p>Exon.RAxML.heterogenous.c123.tre</p></list-item><list-item><p>Exon.RAxML.heterogenous.c12.tre</p></list-item><list-item><p>Exon.RAxML.homogenous.c123.tre</p></list-item><list-item><p>Exon.RAxML.homogenous.c12.tre</p></list-item><list-item><p>Intron.RAxML.heterogenous.tre.txt</p></list-item><list-item><p>Intron.RAxML.homogenous.tre.txt</p></list-item><list-item><p>Intron.RAxML.partitioned.tre</p></list-item><list-item><p>Intron.RAxML.unpartitioned.tre</p></list-item><list-item><p>Intron.MP-EST.binned.tre</p></list-item><list-item><p>Intron.MP-EST.unbinned.tre</p></list-item><list-item><p>TEIT.RAxML.tre</p></list-item><list-item><p>TENT + c3.ExaML.tre</p></list-item><list-item><p>TENT + outgroup.ExaML.tre</p></list-item><list-item><p>TENT.ExaML.100%.tre</p></list-item><list-item><p>TENT.ExaML.25%.tre</p></list-item><list-item><p>TENT.ExaML.50%.tre</p></list-item><list-item><p>TENT.ExaML.75%.tre</p></list-item><list-item><p>UCE.RAxML.unpartitioned.tre</p></list-item><list-item><p>WGT.ExaML.alternative.tre</p></list-item><list-item><p>WGT.ExaML.best.tree</p></list-item></list></p></sec><sec id="Sec28"><title>Newick files of the 11 timetrees (chronograms)</title><p><list list-type="bullet"><list-item><p>Chronogram01.TENT.ExAML.tre</p></list-item><list-item><p>Chronogram02.TENT.ExAML.max865.tre</p></list-item><list-item><p>Chronogram03.TENT.ExAML.Allig247.tre</p></list-item><list-item><p>Chronogram04.TENT.ExAML.no-outgroup.tre</p></list-item><list-item><p>Chronogram05.TENT.ExAML.no-outgroup.max865.tre</p></list-item><list-item><p>Chronogram06.TENT.MP-EST.tre</p></list-item><list-item><p>Chronogram07.WGT.ExAML.alternative.tre</p></list-item><list-item><p>Chronogram08.WGT.ExAML.best.tre</p></list-item><list-item><p>Chronogram09.Intron.ExAML.unpartitioned.tre</p></list-item><list-item><p>Chronogram10.UCE.RAxML.tre</p></list-item><list-item><p>Chronogram11.Exon.c123.RaXML.partitioned.tre</p></list-item></list></p></sec><sec id="Sec29"><title>Newick file downloads of gene trees (species abbreviated with 5-letter names)</title><p><list list-type="bullet"><list-item><p>ML (bestML) gene trees</p></list-item><list-item><p>Bootstrap replicates of ML gene trees</p></list-item><list-item><p>ML (bestML) supergene trees used in MP-EST analyses</p></list-item><list-item><p>Bootstrap replicates of supergene trees used in MP-EST analyses</p></list-item><list-item><p>Partition files showing which loci make up which bins for MP-EST analyses</p></list-item></list></p></sec></sec><sec id="Sec30"><title>List of scripts used in avian phylogenomics project</title><p>We also deposit the key scripts used in this project in GigaDB, which include:<list list-type="bullet"><list-item><p>Script for filtering amino acid alignments</p></list-item><list-item><p>Script for filtering nucleotide sequence alignments</p></list-item><list-item><p>Script for mapping names from 5-letter codes to full names</p></list-item><list-item><p>Scripts related to indel analyses</p></list-item></list></p><p>We provide readme files in the script directories describing the usage of the scripts.</p></sec></sec><sec id="Sec31"><title>Availability and requirements</title><p>Project name: Avian Phylogenomic Project scripts</p><p>Project home page: <ext-link ext-link-type="uri" xlink:href="https://github.com/gigascience/paper-jarvis2014">https://github.com/gigascience/paper-jarvis2014</ext-link>; also see companion paper home page for related data <ext-link ext-link-type="uri" xlink:href="https://github.com/gigascience/paper-zhang2014">https://github.com/gigascience/paper-zhang2014</ext-link></p><p>Operating system: Unix</p><p>Programming language: R, Perl, python</p><p>License: GNU GPL v3.</p><p>Any restrictions to use by non-academics: none</p></sec><sec id="Sec32"><title>Availability of supporting data</title><p>Other data files presented in this data note for the majority of genomes are available in the <italic>GigaScience</italic> repository, GigaDB [<xref ref-type="bibr" rid="CR26">26</xref>] (Table <xref rid="Tab1" ref-type="table">1</xref>), as well as NCBI (Table <xref rid="Tab1" ref-type="table">1</xref>), ENSEMBL, UCSC, and CoGe databases. ENSEMBL: <ext-link ext-link-type="uri" xlink:href="http://avianbase.narf.ac.uk/index.html">http://avianbase.narf.ac.uk/index.html</ext-link> UCSC: (<ext-link ext-link-type="uri" xlink:href="http://genome.ucsc.edu/cgi-bin/hgGateway">http://genome.ucsc.edu/cgi-bin/hgGateway</ext-link>; under vertebrate genomes) CoGe: (<ext-link ext-link-type="uri" xlink:href="https://genomevolution.org/wiki/index.php/Bird_CoGe">https://genomevolution.org/wiki/index.php/Bird_CoGe</ext-link>).</p></sec></body><back><app-group><app id="App1"><sec id="Sec33"><title>Additional file</title><p><media position="anchor" xlink:href="13742_2014_38_MOESM1_ESM.doc" id="MOESM1"><label>Additional file 1:</label><caption><p><bold>Full author list.</bold></p></caption></media></p></sec></app></app-group><glossary><title>Abbreviations</title><def-list><def-list><def-item><term>TE</term><def><p>Transposable element</p></def></def-item><def-item><term>TENT</term><def><p>Total evidence Nucleotide tree</p></def></def-item><def-item><term>TEIT</term><def><p>Total evidence indel tree</p></def></def-item><def-item><term>WGT</term><def><p>Whole genome tree</p></def></def-item><def-item><term>UCE</term><def><p>Ultra conserved element</p></def></def-item><def-item><term>c123</term><def><p>1st, 2nd, and 3rd codons of exons</p></def></def-item></def-list></def-list></glossary><fn-group><fn><p>Erich D Jarvis and Siavash Mirarab contributed equally to this work.</p></fn><fn><p><bold>Competing interests</bold></p><p>The authors declare that they have no competing interests.</p></fn><fn><p><bold>Authors’ contributions</bold></p><p>Coordinated the project EDJ, TW, MTPG, and GZ; Wrote the paper and co-supervised the project EDJ, SM, AJA, PH, TW, MTPG, GZ, ELB, JC, SE, ASt, DPM; Sample coordination and collections JH, EDJ, MTPG, AAN; Alignments SM, AJA, TW, ASt, RdF, MTPG, CL, GZ, BCF, EDJ; Species trees and gene trees AA, SM, ASt, BCF, TW, CL, CCW; Indels PH, NN, AJA; Transposable Elements ASu, HE; Fossil-calibrated chronograms SYWH, PH, MTPG, JC, DM, SE. The contribution information for all authors is provided in Additional file <xref rid="MOESM1" ref-type="media">1</xref>. All authors read and approved the final manuscript.</p></fn></fn-group><ack><title>Acknowledgements</title><p>The majority of genome sequencing and annotation was supported by internal funding from BGI. Additional significant support is from the coordinators of the project: E.D.J. from the Howard Hughes Medical Institute (HHMI) and NIH Directors Pioneer Award DP1OD000448. S.M. from an HHMI International Student Fellowship. G.Z. from Marie Curie International Incoming Fellowship grant (300837); T.W. from NSF DEB 0733029, NSF DBI 1062335, NSF IR/D program; and M.T.P.G. from a Danish National Research Foundation grant (DNRF94) and a Lundbeck Foundation grant (R52-A5062).</p><p>We thank the following Centers that allowed us to conduct the computationally intensive analyses for this study: Heidelberg Institute for Theoretical Studies (HITS); San Diego Supercomputer Center (SDSC), with support by an NSF grant; SuperMUC Petascale System at the Leibniz Supercomputing Center; Technical University of Denmark (DTU); Texas Advanced Computing Center (TACC); Georgia Advanced Computing Resource Center (GACRC), a partnership between the University of Georgia’s Office of the Vice President for Research and Office of the Vice President for Information Technology; Amazon Web Services (AWS); BGI; Nautilus supercomputer at the National Institute for Computational Sciences of the University of Tennessee and Smithsonian; and Duke University Institute for Genome Sciences and Policy.</p><p>The full author list of The Avian Phylogenomics Consortium is provided at the end of the data note.</p></ack><ref-list id="Bib1"><title>References</title><ref id="CR1"><label>1.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jarvis</surname><given-names>ED</given-names></name><name><surname>Mirarab</surname><given-names>S</given-names></name><name><surname>Aberer</surname><given-names>AJ</given-names></name><name><surname>Li</surname><given-names>B</given-names></name><name><surname>Houde</surname><given-names>P</given-names></name><name><surname>Li</surname><given-names>C</given-names></name><etal></etal></person-group><article-title>Whole genome analyses resolve the early branches in the tree of life of modern birds</article-title><source>Science</source><year>2014</year><volume>346</volume><issue>6215</issue><fpage>1320</fpage><lpage>31</lpage><pub-id pub-id-type="doi">10.1126/science.1253451</pub-id><pub-id pub-id-type="pmid">25504713</pub-id></element-citation></ref><ref id="CR2"><label>2.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname><given-names>G</given-names></name><name><surname>Li</surname><given-names>C</given-names></name><name><surname>Li</surname><given-names>Q</given-names></name><name><surname>Li</surname><given-names>B</given-names></name><name><surname>Larkin</surname><given-names>DM</given-names></name><name><surname>Lee</surname><given-names>C</given-names></name><etal></etal></person-group><article-title>Comparative genomics reveal insights into avian genome evolution and adaption</article-title><source>Science</source><year>2014</year><volume>346</volume><issue>6215</issue><fpage>1311</fpage><lpage>20</lpage><pub-id pub-id-type="doi">10.1126/science.1251385</pub-id><pub-id pub-id-type="pmid">25504712</pub-id></element-citation></ref><ref id="CR3"><label>3.</label><mixed-citation publication-type="other">A Stamatakis, AJ Aberer. Novel parallelization schemes for large-scale likelihood-based phylogenetic inference. IEEE 27th International Symposium on Parallel and Distributed Processing, 1195–1204. 2013</mixed-citation></ref><ref id="CR4"><label>4.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Mirarab</surname><given-names>S</given-names></name><name><surname>Bayzid</surname><given-names>MS</given-names></name><name><surname>Boussau</surname><given-names>B</given-names></name><name><surname>Warnow</surname><given-names>T</given-names></name></person-group><article-title>Statistical binning enables an accurate coalescent-based estimation of the avian tree</article-title><source>Science</source><year>2014</year><volume>346</volume><issue>6215</issue><fpage>1</fpage><lpage>9</lpage><pub-id pub-id-type="doi">10.1126/science.1250463</pub-id></element-citation></ref><ref id="CR5"><label>5.</label><mixed-citation publication-type="other">J Cracraft, in The Howard and Moore Complete Checklist of the Birds of the World, E. C. Dickinson, J. V. Remsen, Eds. Eastbourne, U.K.: Aves Press; 2013. pp. xxi-xliii</mixed-citation></ref><ref id="CR6"><label>6.</label><element-citation publication-type="book"><person-group person-group-type="author"><name><surname>Dickinson</surname><given-names>EC</given-names></name><name><surname>Remsen</surname><given-names>JV</given-names></name></person-group><source>Eds</source><year>2013</year><publisher-loc>Aves Press</publisher-loc><publisher-name>The Howard and Moore Complete Checklist of Birds of the World</publisher-name></element-citation></ref><ref id="CR7"><label>7.</label><element-citation publication-type="book"><person-group person-group-type="author"><name><surname>Gill</surname><given-names>F</given-names></name><name><surname>Wright</surname><given-names>M</given-names></name></person-group><source>Birds of the World: Recommended English Names</source><year>2006</year><publisher-loc>Princeton, N.J.</publisher-loc><publisher-name>Princeton University Press</publisher-name></element-citation></ref><ref id="CR8"><label>8.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hillier</surname><given-names>LW</given-names></name><name><surname>Miller</surname><given-names>W</given-names></name><name><surname>Birney</surname><given-names>E</given-names></name><name><surname>Warren</surname><given-names>W</given-names></name><name><surname>Hardison</surname><given-names>RD</given-names></name><name><surname>Ponting</surname><given-names>CP</given-names></name><etal></etal></person-group><article-title>Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution</article-title><source>Nature</source><year>2004</year><volume>432</volume><fpage>695</fpage><lpage>716</lpage><pub-id pub-id-type="doi">10.1038/nature03154</pub-id><pub-id pub-id-type="pmid">15592404</pub-id></element-citation></ref><ref id="CR9"><label>9.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Warren</surname><given-names>WC</given-names></name><name><surname>Clayton</surname><given-names>DF</given-names></name><name><surname>Ellegren</surname><given-names>H</given-names></name><name><surname>Arnold</surname><given-names>AP</given-names></name><name><surname>Hillier</surname><given-names>LW</given-names></name><name><surname>Künstner</surname><given-names>A</given-names></name><etal></etal></person-group><article-title>The genome of a songbird</article-title><source>Nature</source><year>2010</year><volume>464</volume><fpage>757</fpage><lpage>62</lpage><pub-id pub-id-type="doi">10.1038/nature08819</pub-id><pub-id pub-id-type="pmid">20360741</pub-id></element-citation></ref><ref id="CR10"><label>10.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Faircloth</surname><given-names>BC</given-names></name><name><surname>McCormack</surname><given-names>JE</given-names></name><name><surname>Crawford</surname><given-names>NG</given-names></name><name><surname>Harvey</surname><given-names>MG</given-names></name><name><surname>Brumfield</surname><given-names>RT</given-names></name><name><surname>Glenn</surname><given-names>TC</given-names></name></person-group><article-title>Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales</article-title><source>Syst Biol</source><year>2012</year><volume>61</volume><fpage>717</fpage><lpage>26</lpage><pub-id pub-id-type="doi">10.1093/sysbio/sys004</pub-id><pub-id pub-id-type="pmid">22232343</pub-id></element-citation></ref><ref id="CR11"><label>11.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>McCormack</surname><given-names>JE</given-names></name><name><surname>Faircloth</surname><given-names>BC</given-names></name><name><surname>Crawford</surname><given-names>NG</given-names></name><name><surname>Gowaty</surname><given-names>PA</given-names></name><name><surname>Brumfield</surname><given-names>RT</given-names></name><name><surname>Glenn</surname><given-names>TC</given-names></name></person-group><article-title>Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis</article-title><source>Genome Res</source><year>2012</year><volume>22</volume><fpage>746</fpage><lpage>54</lpage><pub-id pub-id-type="doi">10.1101/gr.125864.111</pub-id><pub-id pub-id-type="pmid">22207614</pub-id></element-citation></ref><ref id="CR12"><label>12.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dimitrieva</surname><given-names>S</given-names></name><name><surname>Bucher</surname><given-names>P</given-names></name></person-group><article-title>UCNEbase–a database of ultraconserved non-coding elements and genomic regulatory blocks</article-title><source>Nucleic Acids Res</source><year>2013</year><volume>41</volume><fpage>D101</fpage><lpage>9</lpage><pub-id pub-id-type="doi">10.1093/nar/gks1092</pub-id><pub-id pub-id-type="pmid">23193254</pub-id></element-citation></ref><ref id="CR13"><label>13.</label><element-citation publication-type="book"><person-group person-group-type="author"><name><surname>Harris</surname><given-names>RS</given-names></name></person-group><source>Improved pairwise alignment of genomic DNA. Ph.D. Thesis</source><year>2007</year></element-citation></ref><ref id="CR14"><label>14.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Blanchette</surname><given-names>M</given-names></name><name><surname>Faircloth</surname><given-names>BC</given-names></name><name><surname>Crawford</surname><given-names>NG</given-names></name><name><surname>Gowaty</surname><given-names>PA</given-names></name><name><surname>Brumfield</surname><given-names>RT</given-names></name><name><surname>Glenn</surname><given-names>TC</given-names></name></person-group><article-title>Aligning multiple genomic sequences with the threaded blockset aligner</article-title><source>Genome Res</source><year>2004</year><volume>14</volume><fpage>708</fpage><lpage>15</lpage><pub-id pub-id-type="doi">10.1101/gr.1933104</pub-id><pub-id pub-id-type="pmid">15060014</pub-id></element-citation></ref><ref id="CR15"><label>15.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Simmons</surname><given-names>MP</given-names></name><name><surname>Ochoterena</surname><given-names>H</given-names></name></person-group><article-title>Gaps as characters in sequence-based phylogenetic analyses</article-title><source>Syst Biol</source><year>2000</year><volume>49</volume><fpage>369</fpage><lpage>81</lpage><pub-id pub-id-type="doi">10.1093/sysbio/49.2.369</pub-id><pub-id pub-id-type="pmid">12118412</pub-id></element-citation></ref><ref id="CR16"><label>16.</label><mixed-citation publication-type="other">D. P. Liitle. 2xread: a simple indel coding tool. Program distributed by the author . 2005. <ext-link ext-link-type="uri" xlink:href="http://www.nybg.org/files/scientists/2xread.html">http://www.nybg.org/files/scientists/2xread.html</ext-link>.</mixed-citation></ref><ref id="CR17"><label>17.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Young</surname><given-names>ND</given-names></name><name><surname>Healy</surname><given-names>J</given-names></name></person-group><article-title>GapCoder automates the use of indel characters in phylogenetic analysis</article-title><source>BMC Bioinformatics</source><year>2003</year><volume>4</volume><fpage>6</fpage><pub-id pub-id-type="doi">10.1186/1471-2105-4-6</pub-id><pub-id pub-id-type="pmid">12689349</pub-id></element-citation></ref><ref id="CR18"><label>18.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Katoh</surname><given-names>K</given-names></name><name><surname>Toh</surname><given-names>H</given-names></name></person-group><article-title>Recent developments in the MAFFT multiple sequence alignment program</article-title><source>Brief Bioinform</source><year>2008</year><volume>9</volume><fpage>286</fpage><lpage>98</lpage><pub-id pub-id-type="doi">10.1093/bib/bbn013</pub-id><pub-id pub-id-type="pmid">18372315</pub-id></element-citation></ref><ref id="CR19"><label>19.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Suh</surname><given-names>A</given-names></name><name><surname>Paus</surname><given-names>M</given-names></name><name><surname>Kiefmann</surname><given-names>M</given-names></name><name><surname>Churakov</surname><given-names>G</given-names></name><name><surname>Franke</surname><given-names>FA</given-names></name><name><surname>Brosius</surname><given-names>J</given-names></name><etal></etal></person-group><article-title>Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds</article-title><source>Nat Commun</source><year>2011</year><volume>2</volume><fpage>443</fpage><pub-id pub-id-type="doi">10.1038/ncomms1448</pub-id><pub-id pub-id-type="pmid">21863010</pub-id></element-citation></ref><ref id="CR20"><label>20.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Suh</surname><given-names>A</given-names></name><name><surname>Kriegs</surname><given-names>JO</given-names></name><name><surname>Donnellan</surname><given-names>S</given-names></name><name><surname>Brosius</surname><given-names>J</given-names></name><name><surname>Schmitz</surname><given-names>J</given-names></name></person-group><article-title>A universal method for the study of CR1 retroposons in nonmodel bird genomes</article-title><source>Mol Biol Evol</source><year>2012</year><volume>29</volume><fpage>2899</fpage><lpage>903</lpage><pub-id pub-id-type="doi">10.1093/molbev/mss124</pub-id><pub-id pub-id-type="pmid">22522308</pub-id></element-citation></ref><ref id="CR21"><label>21.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Suh</surname><given-names>A</given-names></name><name><surname>Churakov</surname><given-names>G</given-names></name><name><surname>Ramakodi</surname><given-names>MP</given-names></name><name><surname>Platt</surname><given-names>RN 2nd</given-names></name><name><surname>Jurka</surname><given-names>J</given-names></name><name><surname>Kojima</surname><given-names>KK</given-names></name><name><surname>Caballero</surname><given-names>J</given-names></name><etal></etal></person-group><article-title>Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes</article-title><source>Genome Biol. Evol</source><year>2015</year><volume>7</volume><fpage>205</fpage><lpage>217</lpage><pub-id pub-id-type="doi">10.1093/gbe/evu256</pub-id><pub-id pub-id-type="pmid">25503085</pub-id></element-citation></ref><ref id="CR22"><label>22.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname><given-names>K</given-names></name><name><surname>Warnow</surname><given-names>TJ</given-names></name><name><surname>Holder</surname><given-names>MT</given-names></name><name><surname>Nelesen</surname><given-names>SM</given-names></name><name><surname>Yu</surname><given-names>J</given-names></name><name><surname>Stamatakis</surname><given-names>AP</given-names></name></person-group><article-title>SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees</article-title><source>Syst Biol</source><year>2012</year><volume>61</volume><fpage>90</fpage><lpage>106</lpage><pub-id pub-id-type="doi">10.1093/sysbio/syr095</pub-id><pub-id pub-id-type="pmid">22139466</pub-id></element-citation></ref><ref id="CR23"><label>23.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname><given-names>K</given-names></name><name><surname>Raghavan</surname><given-names>S</given-names></name><name><surname>Nelesen</surname><given-names>S</given-names></name><name><surname>Linder</surname><given-names>CR</given-names></name><name><surname>Warnow</surname><given-names>T</given-names></name></person-group><article-title>Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees</article-title><source>Science</source><year>2009</year><volume>324</volume><fpage>1561</fpage><lpage>4</lpage><pub-id pub-id-type="doi">10.1126/science.1171243</pub-id><pub-id pub-id-type="pmid">19541996</pub-id></element-citation></ref><ref id="CR24"><label>24.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Löytynoja</surname><given-names>A</given-names></name><name><surname>Goldman</surname><given-names>N</given-names></name></person-group><article-title>An algorithm for progressive multiple alignment of sequences with insertions</article-title><source>Proc Natl Acad Sci U S A</source><year>2005</year><volume>102</volume><fpage>10557</fpage><lpage>62</lpage><pub-id pub-id-type="doi">10.1073/pnas.0409137102</pub-id><pub-id pub-id-type="pmid">16000407</pub-id></element-citation></ref><ref id="CR25"><label>25.</label><mixed-citation publication-type="other">Zhang G, Li B, Li C, Gilbert MTP, Jarvis ED, Wang J. The Avian genome Consortium, Wang J: Comparative genomic data of the Avian Phylogenomics Project. GigaSci Database 2014, <ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101000">http://dx.doi.org/10.5524/101000</ext-link></mixed-citation></ref><ref id="CR26"><label>26.</label><mixed-citation publication-type="other">Jarvis ED, Mirarab S, Aberer A, Houde P, Li C, Ho S, et al. Phylogenomic analyses data of the avian phylogenomics project. GigaScience Database. 2014. <ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/101041">http://dx.doi.org/10.5524/101041</ext-link></mixed-citation></ref></ref-list></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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