TY - CHAP AU - Boeke, J. D. AU - Stoye, J. P. ED - Coffin, J. M. ED - Hughes, S. H. ED - Varmus, H. E. PY - 1997 DA - 1997// TI - Retrotransposons, endogenous retroviruses, and the evolution of retroelements BT - Retroviruses PB - CSHL Press CY - New York ID - Boeke1997 ER - TY - CHAP AU - Petropoulos, C. ED - Coffin, J. M. ED - Hughes, S. H. ED - Varmus, H. E. PY - 1997 DA - 1997// TI - Retroviral taxonomy, protein structures, sequences, and genetic maps BT - Retroviruses PB - CSHL Press CY - New York ID - Petropoulos1997 ER - TY - JOUR AU - Gifford, R. AU - Tristem, M. PY - 2003 DA - 2003// TI - The evolution, distribution and diversity of endogenous retroviruses JO - Virus Genes VL - 26 UR - https://doi.org/10.1023/A:1024455415443 DO - 10.1023/A:1024455415443 ID - Gifford2003 ER - TY - JOUR AU - Katzourakis, A. AU - Tristem, M. AU - Pybus, O. G. AU - Gifford, R. J. PY - 2007 DA - 2007// TI - Discovery and analysis of the first endogenous lentivirus JO - Proc Natl Acad Sci USA VL - 104 UR - https://doi.org/10.1073/pnas.0700471104 DO - 10.1073/pnas.0700471104 ID - Katzourakis2007 ER - TY - JOUR AU - Keckesova, Z. AU - Ylinen, L. M. J. AU - Towers, G. J. AU - Gifford, R. J. AU - Katzourakis, A. PY - 2009 DA - 2009// TI - Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses JO - Virology VL - 384 UR - https://doi.org/10.1016/j.virol.2008.10.045 DO - 10.1016/j.virol.2008.10.045 ID - Keckesova2009 ER - TY - JOUR AU - van der Loo, W. AU - Abrantes, J. AU - Esteves, P. J. PY - 2009 DA - 2009// TI - Sharing of endogenous lentiviral gene fragments among leporid lineages separated for more than 12 million years JO - J Virol VL - 83 UR - https://doi.org/10.1128/JVI.01116-08 DO - 10.1128/JVI.01116-08 ID - van der Loo2009 ER - TY - JOUR AU - Stremlau, M. AU - Owens, C. M. AU - Perron, M. J. AU - Kiessling, M. AU - Autissier, P. AU - Sodroski, J. PY - 2004 DA - 2004// TI - The cytoplasmic body component TRIM5α restricts HIV-1 infection in Old World monkeys JO - Nature VL - 427 UR - https://doi.org/10.1038/nature02343 DO - 10.1038/nature02343 ID - Stremlau2004 ER - TY - JOUR AU - Sayah, D. M. AU - Sokolskaja, E. AU - Berthoux, L. AU - Luban, J. PY - 2004 DA - 2004// TI - Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1 JO - Nature VL - 430 UR - https://doi.org/10.1038/nature02777 DO - 10.1038/nature02777 ID - Sayah2004 ER - TY - JOUR AU - Nisole, S. AU - Stoye, J. P. AU - Saïb, A. PY - 2005 DA - 2005// TI - TRIM family proteins: retroviral restriction and antiviral defence JO - Nat Rev Microbiol VL - 3 UR - https://doi.org/10.1038/nrmicro1248 DO - 10.1038/nrmicro1248 ID - Nisole2005 ER - TY - JOUR AU - Ozato, K. AU - Shin, D. -. M. AU - Chang, T. -. H. AU - Morse, H. C. PY - 2008 DA - 2008// TI - TRIM family proteins and their emerging roles in innate immunity JO - Nat Rev Immunol VL - 8 UR - https://doi.org/10.1038/nri2413 DO - 10.1038/nri2413 ID - Ozato2008 ER - TY - JOUR AU - Reymond, A. AU - Meroni, G. AU - Fantozzi, A. AU - Merla, G. AU - Cairo, S. AU - Luzi, L. AU - Riganelli, D. AU - Zanaria, E. AU - Messali, S. AU - Cainarca, S. AU - Guffanti, A. AU - Minucci, S. AU - Pelicci, P. G. AU - Ballabio, A. PY - 2001 DA - 2001// TI - The tripartite motif family identifies cell compartments JO - EMBO J VL - 20 UR - https://doi.org/10.1093/emboj/20.9.2140 DO - 10.1093/emboj/20.9.2140 ID - Reymond2001 ER - TY - JOUR AU - Yamauchi, K. AU - Wada, K. AU - Tanji, K. AU - Tanaka, M. AU - Kamitani, T. PY - 2008 DA - 2008// TI - Ubiquitination of E3 ubiquitin ligase TRIM5α and its potential role JO - FEBS J VL - 275 UR - https://doi.org/10.1111/j.1742-4658.2008.06313.x DO - 10.1111/j.1742-4658.2008.06313.x ID - Yamauchi2008 ER - TY - JOUR AU - Javanbakht, H. AU - Diaz-Griffero, F. AU - Stremlau, M. AU - Si, Z. AU - Sodroski, J. PY - 2005 DA - 2005// TI - The contribution of RING and B-box 2 domains to retroviral restriction mediated by monkey TRIM5alpha JO - J Biol Chem VL - 280 UR - https://doi.org/10.1074/jbc.M502145200 DO - 10.1074/jbc.M502145200 ID - Javanbakht2005 ER - TY - JOUR AU - Li, X. AU - Song, B. AU - Xiang, S. H. AU - Sodroski, J. PY - 2007 DA - 2007// TI - Functional interplay between the B-BOX 2 and the B30.2 (SPRY) domains of TRIM5α JO - Virology VL - 366 UR - https://doi.org/10.1016/j.virol.2007.04.022 DO - 10.1016/j.virol.2007.04.022 ID - Li2007 ER - TY - JOUR AU - Li, X. AU - Sodroski, J. PY - 2008 DA - 2008// TI - The TRIM5alpha B-box 2 domain promotes cooperative binding to the retroviral capsid by mediating higher-order self-association JO - J Virol VL - 82 UR - https://doi.org/10.1128/JVI.01548-08 DO - 10.1128/JVI.01548-08 ID - Li2008 ER - TY - JOUR AU - Javanbakht, H. AU - Yuan, W. AU - Yeung, D. F. AU - Song, B. AU - Diaz-Griffero, F. AU - Li, Y. AU - Li, X. AU - Stremlau, M. AU - Sodroski, J. PY - 2006 DA - 2006// TI - Characterization of TRIM5α trimerization and its contribution to human immunodeficiency virus capsid binding JO - Virology VL - 353 UR - https://doi.org/10.1016/j.virol.2006.05.017 DO - 10.1016/j.virol.2006.05.017 ID - Javanbakht2006 ER - TY - JOUR AU - Yap, M. W. AU - Nisole, S. AU - Stoye, J. P. PY - 2005 DA - 2005// TI - A single amino acid change in the SPRY domain of human Trim5α leads to HIV-1 restriction JO - Curr Biol VL - 15 UR - https://doi.org/10.1016/j.cub.2004.12.042 DO - 10.1016/j.cub.2004.12.042 ID - Yap2005 ER - TY - JOUR AU - Stremlau, M. AU - Perron, M. AU - Welikala, S. AU - Sodroski, J. PY - 2005 DA - 2005// TI - Species-specific variation in the B30.2 (SPRY) domain of TRIM5α determines the potency of Human Immunodeficiency Virus restriction JO - J Virol VL - 79 UR - https://doi.org/10.1128/JVI.79.5.3139-3145.2005 DO - 10.1128/JVI.79.5.3139-3145.2005 ID - Stremlau2005 ER - TY - JOUR AU - Hatziioannou, T. AU - Perez-Caballero, D. AU - Yang, A. AU - Cowan, S. AU - Bieniasz, P. D. PY - 2004 DA - 2004// TI - Retrovirus resistance factors Ref1 and Lv1 are species-specific variants of TRIM5alpha JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0402361101 DO - 10.1073/pnas.0402361101 ID - Hatziioannou2004 ER - TY - JOUR AU - Keckesova, Z. AU - Ylinen, L. M. AU - Towers, G. J. PY - 2004 DA - 2004// TI - The human and African green monkey TRIM5alpha genes encode Ref1 and Lv1 retroviral restriction factor activities JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0402474101 DO - 10.1073/pnas.0402474101 ID - Keckesova2004 ER - TY - JOUR AU - Yap, M. W. AU - Nisole, S. AU - Lynch, C. AU - Stoye, J. P. PY - 2004 DA - 2004// TI - Trim5alpha protein restricts both HIV-1 and murine leukemia virus JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0402876101 DO - 10.1073/pnas.0402876101 ID - Yap2004 ER - TY - JOUR AU - Perron, M. J. AU - Stremlau, M. AU - Song, B. AU - Ulm, W. AU - Mulligan, R. C. AU - Sodroski, J. PY - 2004 DA - 2004// TI - TRIM5alpha mediates the postentry block to N-tropic murine leukemia viruses in human cells JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0403364101 DO - 10.1073/pnas.0403364101 ID - Perron2004 ER - TY - JOUR AU - Li, Y. AU - Li, X. AU - Stremlau, M. AU - Lee, M. AU - Sodrosky, J. PY - 2006 DA - 2006// TI - Removal of arginine 332 allows human TRIM5alpha to bind human immunodeficiency virus capsids and to restrict infection JO - J Virol VL - 80 UR - https://doi.org/10.1128/JVI.00270-06 DO - 10.1128/JVI.00270-06 ID - Li2006 ER - TY - JOUR AU - Sebastian, S. AU - Luban, J. PY - 2005 DA - 2005// TI - TRIM5alpha selectively binds a restriction-sensitive retroviral capsid JO - Retrovirology VL - 2 UR - https://doi.org/10.1186/1742-4690-2-40 DO - 10.1186/1742-4690-2-40 ID - Sebastian2005 ER - TY - JOUR AU - Song, B. AU - Gold, B. AU - O'hUigin, C. AU - Javanbakht, H. AU - Li, X. AU - Stremlau, M. AU - Winkler, C. AU - Dean, M. AU - Sodroski, J. PY - 2005 DA - 2005// TI - The B30.2 (SPRY) domain of the retroviral restriction factor TRIM5alpha exhibits lineage-specific length and sequence variation in primates JO - J Virol VL - 79 UR - https://doi.org/10.1128/JVI.79.10.6111-6121.2005 DO - 10.1128/JVI.79.10.6111-6121.2005 ID - Song2005 ER - TY - JOUR AU - James, L. C. AU - Keeble, A. H. AU - Khan, Z. AU - Rhodes, D. A. AU - Trowsdale, J. PY - 2007 DA - 2007// TI - Structural basis for PRYSPRY-mediated tripartite motif (TRIM) protein function JO - Proc Natl Acad Sci USA VL - 104 UR - https://doi.org/10.1073/pnas.0609174104 DO - 10.1073/pnas.0609174104 ID - James2007 ER - TY - JOUR AU - Tareen, S. U. AU - Emerman, M. PY - 2011 DA - 2011// TI - Human TRIM5α has additional activities that are uncoupled from retroviral capsid recognition JO - Virology VL - 409 UR - https://doi.org/10.1016/j.virol.2010.09.018 DO - 10.1016/j.virol.2010.09.018 ID - Tareen2011 ER - TY - JOUR AU - Pertel, T. AU - Hausmann, S. AU - Morger, D. AU - Züger, S. AU - Guerra, J. AU - Lascano, J. AU - Reinhard, C. AU - Santoni, F. A. AU - Uchil, P. D. AU - Chatel, L. AU - Bisiaux, A. AU - Albert, M. L. AU - Strambio-De-Castillia, C. AU - Mothes, W. AU - Pizzato, M. AU - Grütter, M. G. AU - Luban, J. PY - 2011 DA - 2011// TI - TRIM5 is an innate immune sensor for the retrovirus capsid lattice JO - Nature VL - 472 UR - https://doi.org/10.1038/nature09976 DO - 10.1038/nature09976 ID - Pertel2011 ER - TY - JOUR AU - Ganser-Pornillos, B. K. AU - Chandrasekaran, V. AU - Pornillos, O. AU - Sodroski, J. G. AU - Sundquist, W. I. AU - Yeager, M. PY - 2011 DA - 2011// TI - Hexagonal assembly of a restricting TRIM5alpha protein JO - Proc Natl Acad Sci USA VL - 108 UR - https://doi.org/10.1073/pnas.1013426108 DO - 10.1073/pnas.1013426108 ID - Ganser-Pornillos2011 ER - TY - JOUR AU - Zhao, G. AU - Ke, D. AU - Vu, T. AU - Ahn, J. AU - Shah, V. B. AU - Yang, R. AU - Aiken, C. AU - Charlton, L. M. AU - Gronenborn, A. M. AU - Zhang, P. PY - 2011 DA - 2011// TI - Rhesus TRIM5α disrupts the HIV-1 capsid at the inter-hexamer interfaces JO - PLoS Pathog VL - 7 UR - https://doi.org/10.1371/journal.ppat.1002009 DO - 10.1371/journal.ppat.1002009 ID - Zhao2011 ER - TY - JOUR AU - Sawyer, S. L. AU - Wu, L. I. AU - Emerman, M. AU - Malik, H. S. PY - 2005 DA - 2005// TI - Positive selection of primate TRIM5α identifies a critical species-specific retroviral restriction domain JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0409853102 DO - 10.1073/pnas.0409853102 ID - Sawyer2005 ER - TY - JOUR AU - Johnson, W. E. AU - Sawyer, S. L. PY - 2009 DA - 2009// TI - Molecular evolution of the antiretroviral TRIM5 gene JO - Immunogenetics VL - 61 UR - https://doi.org/10.1007/s00251-009-0358-y DO - 10.1007/s00251-009-0358-y ID - Johnson2009 ER - TY - JOUR AU - Soares, E. A. AU - Menezes, A. N. AU - Schrago, C. G. AU - Moreira, M. A. M. AU - Bonvicino, C. R. AU - Soares, M. A. AU - Seuánez, H. N. PY - 2010 DA - 2010// TI - Evolution of TRIM5α B30.2 (SPRY) domain in New World primates JO - Infect Genet Evol VL - 10 UR - https://doi.org/10.1016/j.meegid.2009.11.012 DO - 10.1016/j.meegid.2009.11.012 ID - Soares2010 ER - TY - JOUR AU - Newman, R. M. AU - Hall, L. AU - Connole, M. AU - Chen, G. -. L. AU - Sato, S. AU - Yuste, E. AU - Diehl, W. AU - Hunter, E. AU - Kaur, A. AU - Miller, G. M. AU - Johnson, W. E. PY - 2006 DA - 2006// TI - Balancing selection and the evolution of functional polymorphism in Old World monkey TRIM5α JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0605838103 DO - 10.1073/pnas.0605838103 ID - Newman2006 ER - TY - JOUR AU - Cagliani, R. AU - Fumagalli, M. AU - Biasin, M. AU - Piacentini, L. AU - Riva, S. AU - Pozzoli, U. AU - Bonaglia, M. C. AU - Bresolin, N. AU - Clerici, M. AU - Sironi, M. PY - 2010 DA - 2010// TI - Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 gene JO - Human Genet VL - 128 UR - https://doi.org/10.1007/s00439-010-0884-6 DO - 10.1007/s00439-010-0884-6 ID - Cagliani2010 ER - TY - JOUR AU - Si, Z. AU - Vandegraaff, N. AU - O'hUigin, C. AU - Song, B. AU - Yuan, W. AU - Xu, C. AU - Perron, M. AU - Li, X. AU - Marasco, W. A. AU - Engelman, A. AU - Dean, M. AU - Sodroski, J. PY - 2006 DA - 2006// TI - Evolution of a cytoplasmic tripartite motif (TRIM) protein in cows that restricts retroviral infection JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0600771103 DO - 10.1073/pnas.0600771103 ID - Si2006 ER - TY - JOUR AU - Sawyer, S. L. AU - Emerman, M. AU - Malik, H. S. PY - 2007 DA - 2007// TI - Discordant evolution of the adjacent antiretroviral genes TRIM22 and TRIM5 in mammals JO - PLoS Pathog VL - 3 UR - https://doi.org/10.1371/journal.ppat.0030197 DO - 10.1371/journal.ppat.0030197 ID - Sawyer2007 ER - TY - JOUR AU - Schaller, T. AU - Hué, S. AU - Towers, G. J. PY - 2007 DA - 2007// TI - An active TRIM5 protein in rabbits indicates a common antiviral ancestor for mammalian TRIM5 proteins JO - J Virol VL - 81 UR - https://doi.org/10.1128/JVI.01468-07 DO - 10.1128/JVI.01468-07 ID - Schaller2007 ER - TY - JOUR AU - Tareen, S. U. AU - Sawyer, S. L. AU - Malik, H. S. AU - Emerman, M. PY - 2009 DA - 2009// TI - An expanded clade of rodent Trim5 genes JO - Virology VL - 385 UR - https://doi.org/10.1016/j.virol.2008.12.018 DO - 10.1016/j.virol.2008.12.018 ID - Tareen2009 ER - TY - JOUR AU - Fletcher, A. J. AU - Hué, S. AU - Schaller, T. AU - Pillay, D. AU - Towers, G. J. PY - 2010 DA - 2010// TI - Hare TRIM5α restricts divergent retroviruses and exhibits significant sequence variation from closely related Lagomorpha TRIM5 genes JO - J Virol VL - 84 UR - https://doi.org/10.1128/JVI.01514-10 DO - 10.1128/JVI.01514-10 ID - Fletcher2010 ER - TY - JOUR AU - Matthee, C. A. AU - van Vuuren, B. J. AU - Bell, D. AU - Robinson, T. J. PY - 2004 DA - 2004// TI - A molecular supermatrix of the rabbits and hares (Leporidae) allows for the identification of five intercontinental exchanges during the Miocene JO - Syst Biol VL - 53 UR - https://doi.org/10.1080/10635150490445715 DO - 10.1080/10635150490445715 ID - Matthee2004 ER - TY - CHAP AU - Matthee, C. A. ED - Hedges, S. B. ED - Kumar, S. PY - 2009 DA - 2009// TI - Pikas, hares and rabbits (Lagomorpha) BT - The timetree of life PB - Oxford University Press CY - New York, NY ID - Matthee2009 ER - TY - JOUR AU - Lanier, H. C. AU - Olson, L. E. PY - 2009 DA - 2009// TI - Inferring divergence times within pikas (Ochotona spp.) using mtDNA and relaxed molecular dating techniques JO - Mol Phylogenet Evol VL - 53 UR - https://doi.org/10.1016/j.ympev.2009.05.035 DO - 10.1016/j.ympev.2009.05.035 ID - Lanier2009 ER - TY - CHAP AU - Ferrand, N. AU - Branco, M. ED - Weiss, S. ED - Ferrand, N. PY - 2007 DA - 2007// TI - The evolutionary history of the European rabbit (Oryctolagus cuniculus): major patterns of population differentiation and geographic expansion inferred from protein polymorphism BT - Phylogeography of Southern European Refugia PB - Springer CY - The Netherlands UR - https://doi.org/10.1007/1-4020-4904-8_7 DO - 10.1007/1-4020-4904-8_7 ID - Ferrand2007 ER - TY - JOUR AU - Carmo, C. R. AU - Esteves, P. J. AU - Ferrand, N. AU - van der Loo, W. PY - 2006 DA - 2006// TI - Genetic variation at chemokine receptor CCR5 in leporids: alteration at the 2nd extracellular domain by gene conversion with CCR2 in Oryctolagus, but not in Sylvilagus and Lepus species JO - Immunogenetics VL - 58 UR - https://doi.org/10.1007/s00251-006-0095-4 DO - 10.1007/s00251-006-0095-4 ID - Carmo2006 ER - TY - JOUR AU - Abrantes, J. AU - Carmo, C. R. AU - Matthee, C. A. AU - Yamada, F. AU - van der Loo, W. AU - Esteves, P. J. PY - 2011 DA - 2011// TI - A shared unusual genetic change at the chemokine receptor type 5 between Oryctolagus, Bunolagus and Pentalagus JO - Conserv Genet VL - 12 UR - https://doi.org/10.1007/s10592-009-9990-1 DO - 10.1007/s10592-009-9990-1 ID - Abrantes2011 ER - TY - JOUR AU - Esteves, P. J. AU - Lanning, D. AU - Ferrand, N. AU - Knight, K. L. AU - Zhai, S. K. AU - van der Loo, W. PY - 2005 DA - 2005// TI - The evolution of the immunoglobulin heavy chain variable region (IgVH) in Leporids: an unusual case of transspecies polymorphism JO - Immunogenetics VL - 57 UR - https://doi.org/10.1007/s00251-005-0022-0 DO - 10.1007/s00251-005-0022-0 ID - Esteves2005 ER - TY - JOUR AU - Siepel, A. PY - 2009 DA - 2009// TI - Phylogenomics of primates and their ancestral populations JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.084228.108 DO - 10.1101/gr.084228.108 ID - Siepel2009 ER - TY - JOUR AU - Takahata, N. AU - Satta, Y. PY - 1997 DA - 1997// TI - Evolution of the primate lineage leading to modern humans: phylogenetic and demographic inferences from DNA sequences JO - Proc Natl Acad Sci USA VL - 94 UR - https://doi.org/10.1073/pnas.94.9.4811 DO - 10.1073/pnas.94.9.4811 ID - Takahata1997 ER - TY - JOUR AU - Nei, M. AU - Gojobori, T. PY - 1986 DA - 1986// TI - Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions JO - Mol Biol Evol VL - 3 ID - Nei1986 ER - TY - JOUR AU - Johnson, W. E. AU - Coffin, J. M. PY - 1999 DA - 1999// TI - Constructing primate phylogenies from ancient retrovirus sequences JO - Proc Natl Acad Sci USA VL - 96 UR - https://doi.org/10.1073/pnas.96.18.10254 DO - 10.1073/pnas.96.18.10254 ID - Johnson1999 ER - TY - JOUR AU - Emerman, M. AU - Malik, H. S. PY - 2010 DA - 2010// TI - Paleovirology - Modern consequences of ancient viruses JO - PLoS Biol VL - 8 UR - https://doi.org/10.1371/journal.pbio.1000301 DO - 10.1371/journal.pbio.1000301 ID - Emerman2010 ER - TY - JOUR AU - Kerns, J. A. AU - Emerman, M. AU - Malik, H. S. PY - 2008 DA - 2008// TI - Positive selection and increased antiviral activity associated with the PARP-containing isoform of human zinc-finger antiviral protein JO - PLoS Genet VL - 4 UR - https://doi.org/10.1371/journal.pgen.0040021 DO - 10.1371/journal.pgen.0040021 ID - Kerns2008 ER - TY - JOUR AU - Elde, N. C. AU - Child, S. J. AU - Geballe, A. P. AU - Malik, H. S. PY - 2009 DA - 2009// TI - Protein kinase R reveals an evolutionary model for defeating viral mimicry JO - Nature VL - 457 UR - https://doi.org/10.1038/nature07529 DO - 10.1038/nature07529 ID - Elde2009 ER - TY - JOUR AU - Kaiser, S. M. AU - Malik, H. S. AU - Emerman, M. PY - 2007 DA - 2007// TI - Restriction of an extinct retrovirus by the human TRIM5α antiviral protein JO - Science VL - 316 UR - https://doi.org/10.1126/science.1140579 DO - 10.1126/science.1140579 ID - Kaiser2007 ER - TY - JOUR AU - Goldstone, D. C. AU - Yap, M. W. AU - Robertson, L. E. AU - Haire, L. F. AU - Taylor, W. R. AU - Katzourakis, A. AU - Stoye, J. P. AU - Taylor, I. A. PY - 2010 DA - 2010// TI - Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface JO - Cell Host Microbe VL - 8 UR - https://doi.org/10.1016/j.chom.2010.08.006 DO - 10.1016/j.chom.2010.08.006 ID - Goldstone2010 ER - TY - JOUR AU - Gamble, T. R. AU - Vajdos, F. F. AU - Yoo, S. AU - Worthylake, D. K. AU - Houseweart, M. AU - Sundquist, W. I. AU - Hill, C. P. PY - 1996 DA - 1996// TI - Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV-1 capsid JO - Cell VL - 87 UR - https://doi.org/10.1016/S0092-8674(00)81823-1 DO - 10.1016/S0092-8674(00)81823-1 ID - Gamble1996 ER - TY - JOUR AU - Luban, J. AU - Bossolt, K. L. AU - Franke, E. K. AU - Kalpana, G. V. AU - Goff, S. P. PY - 1993 DA - 1993// TI - Human immunodeficiency virus type 1 Gag protein binds to cyclophilins A and B JO - Cell VL - 73 UR - https://doi.org/10.1016/0092-8674(93)90637-6 DO - 10.1016/0092-8674(93)90637-6 ID - Luban1993 ER - TY - JOUR AU - Krug, M. S. AU - Berger, S. L. PY - 1987 DA - 1987// TI - First-strand cDNA synthesis primed with oligo(dT) JO - Methods Enzymol VL - 152 UR - https://doi.org/10.1016/0076-6879(87)52036-5 DO - 10.1016/0076-6879(87)52036-5 ID - Krug1987 ER - TY - CHAP AU - Zwickl, D. J. PY - 2006 DA - 2006// TI - Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion BT - PhD thesis PB - University of Texas CY - Austin ID - Zwickl2006 ER - TY - JOUR AU - Posada, D. PY - 2008 DA - 2008// TI - jModelTest: Phylogenetic Model Averaging JO - Mol Biol Evol VL - 25 UR - https://doi.org/10.1093/molbev/msn083 DO - 10.1093/molbev/msn083 ID - Posada2008 ER - TY - JOUR AU - Jones, D. T. AU - Taylor, W. R. AU - Thornton, J. M. PY - 1992 DA - 1992// TI - The rapid generation of mutation data matrices from protein sequences JO - CABIOS VL - 8 ID - Jones1992 ER - TY - JOUR AU - Abascal, F. AU - Zardoya, R. AU - Posada, D. PY - 2005 DA - 2005// TI - ProtTest: Selection of best-fit models of protein evolution JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti263 DO - 10.1093/bioinformatics/bti263 ID - Abascal2005 ER - TY - JOUR AU - Drummond, A. AU - Strimmer, K. PY - 2001 DA - 2001// TI - PAL: An object-oriented programming library for molecular evolution and phylogenetics JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.7.662 DO - 10.1093/bioinformatics/17.7.662 ID - Drummond2001 ER - TY - JOUR AU - Guindon, S. AU - Gascuel, O. PY - 2003 DA - 2003// TI - A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood JO - Syst Biol VL - 52 UR - https://doi.org/10.1080/10635150390235520 DO - 10.1080/10635150390235520 ID - Guindon2003 ER - TY - JOUR AU - Fares, M. A. AU - Elena, S. F. AU - Ortiz, J. AU - Moya, A. AU - Barrio, E. PY - 2002 DA - 2002// TI - A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses JO - J Mol Evol VL - 55 UR - https://doi.org/10.1007/s00239-002-2346-9 DO - 10.1007/s00239-002-2346-9 ID - Fares2002 ER - TY - JOUR AU - Kosakovsky Pond, S. L. AU - Frost, S. D. PY - 2005 DA - 2005// TI - Not so different after all: a comparison of methods for detecting amino acid sites under selection JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi105 DO - 10.1093/molbev/msi105 ID - Kosakovsky Pond2005 ER - TY - JOUR AU - Kosakovsky Pond, S. L. AU - Frost, S. D. PY - 2005 DA - 2005// TI - Datamonkey: rapid detection of selective pressure on individual sites of codon alignments JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti320 DO - 10.1093/bioinformatics/bti320 ID - Kosakovsky Pond2005 ER - TY - JOUR AU - Tamura, K. AU - Peterson, D. AU - Peterson, N. AU - Stecher, G. AU - Nei, M. AU - Kumar, S. PY - 2011 DA - 2011// TI - MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods JO - Mol Biol Evol VL - 28 UR - https://doi.org/10.1093/molbev/msr121 DO - 10.1093/molbev/msr121 ID - Tamura2011 ER - TY - JOUR AU - Tajima, F. PY - 1991 DA - 1991// TI - Determination of window size for analysing DNA sequences JO - J Mol Evol VL - 33 UR - https://doi.org/10.1007/BF02103140 DO - 10.1007/BF02103140 ID - Tajima1991 ER - TY - JOUR AU - Librado, P. AU - Rozas, J. PY - 2009 DA - 2009// TI - DnaSP v5: A software for comprehensive analysis of DNA polymorphism data JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp187 DO - 10.1093/bioinformatics/btp187 ID - Librado2009 ER -