TY - JOUR AU - Asche, F. AU - Hansen, H. AU - Tveteras, R. AU - Tveteras, S. PY - 2009 DA - 2009// TI - The Salmon Disease Crisis in Chile JO - Mar Resour Econ VL - 24 UR - https://doi.org/10.1086/mre.24.4.42629664 DO - 10.1086/mre.24.4.42629664 ID - Asche2009 ER - TY - JOUR AU - Bouchard, D. AU - Keleher, W. AU - Opitz, H. M. AU - Blake, S. AU - Edwards, K. C. AU - Nicholson, B. L. PY - 1999 DA - 1999// TI - Isolation of infectious salmon anemia virus (ISAV) from Atlantic salmon in New Brunswick, Canada JO - Dis Aquat Organ VL - 35 UR - https://doi.org/10.3354/dao035131 DO - 10.3354/dao035131 ID - Bouchard1999 ER - TY - CHAP AU - Geoghegan, F. PY - 2002 DA - 2002// TI - First isolation and identification of ISAV in Ireland BT - 6th Annual Meeting of EU National Reference Laboratories for Fish Diseases. Brussels, Belgium ID - Geoghegan2002 ER - TY - JOUR AU - Kibenge, F. S. B. AU - Munir, K. AU - Kibenge, M. J. T. AU - Joseph, T. AU - Moneke, E. PY - 2004 DA - 2004// TI - Infectious salmon anemia virus: causative agent, pathogenesis and immunity JO - Anim Health Res Rev VL - 5 UR - https://doi.org/10.1079/AHR200461 DO - 10.1079/AHR200461 ID - Kibenge2004 ER - TY - JOUR AU - Lovely, J. AU - Dannevig, B. AU - Falk, K. AU - Hutchin, L. AU - MacKinnon, A. AU - Melville, K. AU - Rimstad, E. AU - Griffiths, S. PY - 1999 DA - 1999// TI - First identification of infectious salmon anaemia virus in North America with haemorrhagic kidney syndrome JO - Dis Aquat Organ VL - 35 UR - https://doi.org/10.3354/dao035145 DO - 10.3354/dao035145 ID - Lovely1999 ER - TY - JOUR AU - Godoy, M. AU - Aedo, A. AU - Kibenge, M. AU - Groman, D. AU - Yason, C. AU - Grothusen, H. AU - Lisperguer, A. AU - Calbucura, M. AU - Avendano, F. AU - Imilan, M. PY - 2008 DA - 2008// TI - First detection, isolation and molecular characterization of infectious salmon anaemia virus associated with clinical disease in farmed Atlantic salmon (Salmo salar) in Chile JO - BMC Vet Res VL - 4 UR - https://doi.org/10.1186/1746-6148-4-28 DO - 10.1186/1746-6148-4-28 ID - Godoy2008 ER - TY - CHAP AU - Kawaoka, Y. AU - Cox, N. AU - Haller, O. AU - Hongo, S. AU - Kaverin, N. AU - Klenk, H. AU - Lamb, R. AU - McCauley, J. AU - Palese, P. AU - Rimstad, E. PY - 2005 DA - 2005// BT - Infectious Salmon Anaemia Virus - Eight Report of the International Committee on Taxonomy Viruses PB - Elsevier Academic Press CY - New York ID - Kawaoka2005 ER - TY - JOUR AU - Cottet, L. AU - Rivas-Aravena, A. AU - Cortez-San Martin, M. AU - Sandino, A. M. AU - Spencer, E. PY - 2010 DA - 2010// TI - Infectious salmon anemia virus--genetics and pathogenesis JO - Virus Res VL - 155 UR - https://doi.org/10.1016/j.virusres.2010.10.021 DO - 10.1016/j.virusres.2010.10.021 ID - Cottet2010 ER - TY - JOUR AU - García-Rosado, E. AU - Markussen, T. AU - Kileng, O. AU - Baekkevold, E. S. AU - Robertsen, B. AU - Mjaaland, S. AU - Rimstad, E. PY - 2008 DA - 2008// TI - Molecular and functional characterization of two infectious salmon anaemia virus (ISAV) proteins with type I interferon antagonizing activity JO - Virus Res VL - 133 UR - https://doi.org/10.1016/j.virusres.2008.01.008 DO - 10.1016/j.virusres.2008.01.008 ID - García-Rosado2008 ER - TY - JOUR AU - Rimstad, E. AU - Mjaaland, S. PY - 2002 DA - 2002// TI - Infectious salmon anaemia virus. An orthomyxovirus causing en emerging infection in Atlantic salmon JO - APMIS VL - 110 UR - https://doi.org/10.1034/j.1600-0463.2002.100401.x DO - 10.1034/j.1600-0463.2002.100401.x ID - Rimstad2002 ER - TY - JOUR AU - Kibenge, F. S. AU - Xu, H. AU - Kibenge, M. AU - Qian, B. AU - Joseph, T. PY - 2007 DA - 2007// TI - Characterization of gene expression on genomic segment 7 of infectious salmon anaemia virus JO - Virology J VL - 4 UR - https://doi.org/10.1186/1743-422X-4-34 DO - 10.1186/1743-422X-4-34 ID - Kibenge2007 ER - TY - JOUR AU - Mjaaland, S. AU - Hungnes, O. AU - Teig, A. AU - Dannevig, B. H. AU - Thorud, K. AU - Rimstad, E. PY - 2002 DA - 2002// TI - Polymorphism in the infectious salmon anemia virus hemagglutinin gene: importance and possible implications for evolution and ecology of infectious salmon anemia disease JO - Virology VL - 304 UR - https://doi.org/10.1006/viro.2002.1658 DO - 10.1006/viro.2002.1658 ID - Mjaaland2002 ER - TY - JOUR AU - Markussen, T. AU - Jonassen, C. M. AU - Numanovic, S. AU - Braaen, S. AU - Hjortaas, M. AU - Nilsen, H. AU - Mjaaland, S. PY - 2008 DA - 2008// TI - Evolutionary mechanisms involved in the virulence of infectious salmon anaemia virus (ISAV), a piscine orthomyxovirus JO - Virology VL - 374 UR - https://doi.org/10.1016/j.virol.2008.01.019 DO - 10.1016/j.virol.2008.01.019 ID - Markussen2008 ER - TY - JOUR AU - Kibenge, F. S. B. AU - Kibenge, M. J. T. AU - Wang, Y. AU - Qian, B. AU - Hariharan, S. AU - Sandi PY - 2007 DA - 2007// TI - Mapping of putative virulence motifs on infectious salmon anemia virus surface glycoprotein genes JO - J Gen Virol VL - 88 UR - https://doi.org/10.1099/vir.0.83097-0 DO - 10.1099/vir.0.83097-0 ID - Kibenge2007 ER - TY - JOUR AU - Cottet, L. AU - Cortez-San Martín, M. AU - Tello, M. AU - Olivares, E. AU - Rivas-Aravena, A. AU - Vallejos, E. AU - Sandino, A. M. AU - Spencer, E. PY - 2010 DA - 2010// TI - Bioinformatic Analysis of the Genome of Infectious Salmon Anemia Viruses associated with outbreaks of high mortality in Chile JO - J Virol VL - 84 UR - https://doi.org/10.1128/JVI.01202-10 DO - 10.1128/JVI.01202-10 ID - Cottet2010 ER - TY - JOUR AU - Nylund, A. AU - Devold, M. AU - Karlsen, M. PY - 2006 DA - 2006// TI - Sequence analysis of the fusion protein gene from infectious salmon anemia virus isolates: evidence of recombination and reassortment JO - J Gen Virol VL - 87 ID - Nylund2006 ER - TY - JOUR AU - Aspehaug, V. AU - Mikalsen, A. B. AU - Snow, M. AU - Biering, E. AU - Villoing, S. PY - 2005 DA - 2005// TI - Characterization of the infectious salmon anemia virus fusion protein JO - J Virol VL - 79 UR - https://doi.org/10.1128/JVI.79.19.12544-12553.2005 DO - 10.1128/JVI.79.19.12544-12553.2005 ID - Aspehaug2005 ER - TY - JOUR AU - Kibenge, F. S. B. AU - Grate, O. N. AU - Johnson, G. AU - Arriagada, R. AU - Kibenge, M. J. T. AU - Wadowska, D. PY - 2001 DA - 2001// TI - Isolation and identification of infectious salmon anaemia virus (ISAV) from Coho salmon in Chile JO - Dis Aquat Organ VL - 45 UR - https://doi.org/10.3354/dao045009 DO - 10.3354/dao045009 ID - Kibenge2001 ER - TY - JOUR AU - Vike, S. AU - Nylund, S. AU - Nylund, A. PY - 2009 DA - 2009// TI - ISA virus in Chile: evidence of vertical transmission JO - Arch Virol VL - 154 UR - https://doi.org/10.1007/s00705-008-0251-2 DO - 10.1007/s00705-008-0251-2 ID - Vike2009 ER - TY - JOUR AU - Kibenge, F. AU - Godoy, M. AU - Wang, Y. AU - Kibenge, M. AU - Gherardelli, V. AU - Mansilla, S. AU - Lisperger, A. AU - Jarpa, M. AU - Larroquete, G. AU - Avendano, F. PY - 2009 DA - 2009// TI - Infectious salmon anaemia virus (ISAV) isolated from the ISA disease outbreaks in Chile diverged from ISAV isolates from Norway around 1996 and was disseminated around 2005, based on surface glycoprotein gene sequences JO - Virology J VL - 6 UR - https://doi.org/10.1186/1743-422X-6-88 DO - 10.1186/1743-422X-6-88 ID - Kibenge2009 ER - TY - JOUR AU - Elena, S. F. AU - Bedhomme, S. AU - Carrasco, P. AU - Cuevas, J. M. AU - de la Iglesia, F. AU - Lafforgue, G. AU - Lalić, J. AU - Pròsper, A. AU - Tromas, N. AU - Zwart, M. P. PY - 2011 DA - 2011// TI - The evolutionary genetics of emerging plant RNA viruses JO - Mol Plant Microbe Interact VL - 24 UR - https://doi.org/10.1094/MPMI-09-10-0214 DO - 10.1094/MPMI-09-10-0214 ID - Elena2011 ER - TY - JOUR AU - Castao, A. AU - Ruiz, L. AU - Elena, S. F. AU - Hernández, C. PY - 2011 DA - 2011// TI - Population differentiation and selective constraints in Pelargonium line pattern virus JO - Virus Research VL - 155 UR - https://doi.org/10.1016/j.virusres.2010.10.022 DO - 10.1016/j.virusres.2010.10.022 ID - Castao2011 ER - TY - JOUR AU - Wu, B. AU - Alexandra AU - Liu, Y. AU - Zhou, G. AU - Wang, X. AU - Elena, S. F. PY - 2011 DA - 2011// TI - Dynamics of molecular evolution and phylogeography of Barley yellow dwarf virus-PAV JO - PloS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0016896 DO - 10.1371/journal.pone.0016896 ID - Wu2011 ER - TY - JOUR AU - Lalić, J. AU - Agudelo-Romero, P. AU - Carrasco, P. AU - Elena, S. F. PY - 2010 DA - 2010// TI - Adaptation of tobacco etch potyvirus to a susceptible ecotype of Arabidopsis thaliana capacitates it for systemic infection of resistant ecotypes JO - Philos Trans R Soc Lond B Biol Sci VL - 365 UR - https://doi.org/10.1098/rstb.2010.0044 DO - 10.1098/rstb.2010.0044 ID - Lalić2010 ER - TY - JOUR AU - Bhatt, S. AU - Holmes, E. C. AU - Pybus, O. G. PY - 2011 DA - 2011// TI - The genomic rate of molecular adaptation of the human influenza A virus JO - Mol Biol Evol VL - 28 UR - https://doi.org/10.1093/molbev/msr044 DO - 10.1093/molbev/msr044 ID - Bhatt2011 ER - TY - JOUR AU - Rambaut, A. AU - Pybus, O. G. AU - Nelson, M. I. AU - Viboud, C. AU - Taubenberger, J. K. AU - Holmes, E. C. PY - 2008 DA - 2008// TI - The genomic and epidemiological dynamics of human influenza A virus JO - Nature VL - 453 UR - https://doi.org/10.1038/nature06945 DO - 10.1038/nature06945 ID - Rambaut2008 ER - TY - JOUR AU - Akaike, H. PY - 1974 DA - 1974// TI - A new look at the statistical model identification JO - IEEE Trans Automat Contr VL - 19 UR - https://doi.org/10.1109/TAC.1974.1100705 DO - 10.1109/TAC.1974.1100705 ID - Akaike1974 ER - TY - JOUR AU - Felsenstein, J. PY - 1992 DA - 1992// TI - Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates JO - Genet Res VL - 59 UR - https://doi.org/10.1017/S0016672300030354 DO - 10.1017/S0016672300030354 ID - Felsenstein1992 ER - TY - JOUR AU - Hughes, G. J. AU - Fearnhill, E. AU - Dunn, D. AU - Lycett, S. J. AU - Rambaut, A. AU - Leigh Brown, A. J. PY - 2009 DA - 2009// TI - Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom JO - Plos Pathog VL - 5 UR - https://doi.org/10.1371/journal.ppat.1000590 DO - 10.1371/journal.ppat.1000590 ID - Hughes2009 ER - TY - JOUR AU - Bennett, S. N. AU - Drummond, A. J. AU - Kapan, D. D. AU - Suchard, M. A. AU - Munoz-Jordan, J. L. AU - Pybus, O. G. AU - Holmes, E. C. AU - Gubler, D. J. PY - 2010 DA - 2010// TI - Epidemic Dynamics Revealed in Dengue Evolution JO - Mol Biol Evol VL - 27 UR - https://doi.org/10.1093/molbev/msp285 DO - 10.1093/molbev/msp285 ID - Bennett2010 ER - TY - JOUR AU - Tazi, L. AU - Pérez-Losada, M. AU - Gu, W. AU - Yang, Y. AU - Xue, L. AU - Crandall, K. AU - Viscidi, R. PY - 2010 DA - 2010// TI - Population dynamics of Neisseria gonorrhoeae in Shanghai, China: a comparative study JO - BMC Infectious Diseases VL - 10 UR - https://doi.org/10.1186/1471-2334-10-13 DO - 10.1186/1471-2334-10-13 ID - Tazi2010 ER - TY - JOUR AU - Zehender, G. AU - De Maddalena, C. AU - Giambelli, C. AU - Milazzo, L. AU - Schiavini, M. AU - Bruno, R. AU - Tanzi, E. AU - Galli, M. PY - 2008 DA - 2008// TI - Different evolutionary rates and epidemic growth of hepatitis B virus genotypes A and D JO - Virology VL - 380 UR - https://doi.org/10.1016/j.virol.2008.07.009 DO - 10.1016/j.virol.2008.07.009 ID - Zehender2008 ER - TY - JOUR AU - Holmes, E. C. PY - 2009 DA - 2009// TI - The Evolutionary Genetics of Emerging Viruses JO - Annu Rev Ecol Evol S VL - 40 UR - https://doi.org/10.1146/annurev.ecolsys.110308.120248 DO - 10.1146/annurev.ecolsys.110308.120248 ID - Holmes2009 ER - TY - JOUR AU - Posada, D. AU - Crandall, K. A. AU - Holmes, E. C. PY - 2002 DA - 2002// TI - Recombination in evolutionary genomics JO - Annu Rev Genet VL - 36 UR - https://doi.org/10.1146/annurev.genet.36.040202.111115 DO - 10.1146/annurev.genet.36.040202.111115 ID - Posada2002 ER - TY - JOUR AU - Boni, M. F. AU - de Jong, M. D. AU - van Doorn, H. R. AU - Holmes, E. C. PY - 2010 DA - 2010// TI - Guidelines for Identifying Homologous Recombination Events in Influenza A Virus JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0010434 DO - 10.1371/journal.pone.0010434 ID - Boni2010 ER - TY - JOUR AU - Boni, M. F. AU - Zhou, Y. AU - Taubenberger, J. K. AU - Holmes, E. C. PY - 2008 DA - 2008// TI - Homologous Recombination Is Very Rare or Absent in Human Influenza A Virus JO - J Virol VL - 82 UR - https://doi.org/10.1128/JVI.02683-07 DO - 10.1128/JVI.02683-07 ID - Boni2008 ER - TY - JOUR AU - He, C. Q. AU - Han, G. Z. AU - Wang, D. AU - Liu, W. AU - Li, G. R. AU - Liu, X. P. AU - Ding, N. Z. PY - 2008 DA - 2008// TI - Homologous recombination evidence in human and swine influenza A viruses JO - Virology VL - 380 UR - https://doi.org/10.1016/j.virol.2008.07.014 DO - 10.1016/j.virol.2008.07.014 ID - He2008 ER - TY - JOUR AU - Kosakovsky Pond, S. L. AU - Posada, D. AU - Stawiski, E. AU - Chappey, C. AU - Poon, A. F. Y. AU - Hughes, G. AU - Fearnhill, E. AU - Gravenor, M. B. AU - Leigh Brown, A. J. AU - Frost, S. D. W. PY - 2009 DA - 2009// TI - An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1 JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000581 DO - 10.1371/journal.pcbi.1000581 ID - Kosakovsky Pond2009 ER - TY - JOUR AU - Martin, D. P. AU - Lemey, P. AU - Lott, M. AU - Moulton, V. AU - Posada, D. AU - Lefeuvre, P. PY - 2010 DA - 2010// TI - RDP3: a flexible and fast computer program for analyzing recombination JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq467 DO - 10.1093/bioinformatics/btq467 ID - Martin2010 ER - TY - JOUR AU - Devold, M. AU - Falk, K. AU - Dale, B. AU - Krossøy, B. AU - Biering, E. AU - Aspehaug, V. AU - Nilsen, F. AU - Nylund, A. PY - 2001 DA - 2001// TI - Strain variation, based on the hemagglutinin gene, in Norwegian ISA virus isolates collected from 1987 to 2001: indications of recombination JO - Dis Aquat Organ VL - 47 UR - https://doi.org/10.3354/dao047119 DO - 10.3354/dao047119 ID - Devold2001 ER - TY - JOUR AU - Cunningham, C. O. AU - Gregory, A. AU - Black, J. AU - Simpson, I. AU - Raynard, R. S. PY - 2002 DA - 2002// TI - A novel variant of the infectious salmon anaemia virus (ISAV) haemagglutinin gene suggests mechanisms for virus diversity JO - Bull Eur Assoc Fish Pathol VL - 22 ID - Cunningham2002 ER - TY - JOUR AU - Posada, D. PY - 2001 DA - 2001// TI - Unveiling the molecular clock in the presence of recombination JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003738 DO - 10.1093/oxfordjournals.molbev.a003738 ID - Posada2001 ER - TY - JOUR AU - Posada, D. AU - Crandall, K. A. PY - 2002 DA - 2002// TI - The effect of recombination on the accuracy of phylogeny estimation JO - J Mol Evol VL - 54 UR - https://doi.org/10.1007/s00239-001-0034-9 DO - 10.1007/s00239-001-0034-9 ID - Posada2002 ER - TY - JOUR AU - Domingo-Calap, P. AU - Sanjuán, R. PY - 2011 DA - 2011// TI - Experimental Evolution of RNA versus DNA Viruses JO - Evolution VL - 65 UR - https://doi.org/10.1111/j.1558-5646.2011.01339.x DO - 10.1111/j.1558-5646.2011.01339.x ID - Domingo-Calap2011 ER - TY - JOUR AU - Drummond, A. J. AU - Rambaut, A. AU - Shapiro, B. AU - Pybus, O. PY - 2005 DA - 2005// TI - Bayesian coalescent inference of past population dynamics from molecular sequences JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi103 DO - 10.1093/molbev/msi103 ID - Drummond2005 ER - TY - JOUR AU - Ho, S. AU - Shapiro, B. PY - 2011 DA - 2011// TI - Skyline-plot methods for estimating demographic history from nucleotide sequences JO - Mol Ecol Resour VL - 11 UR - https://doi.org/10.1111/j.1755-0998.2011.02988.x DO - 10.1111/j.1755-0998.2011.02988.x ID - Ho2011 ER - TY - JOUR AU - Pannell, J. R. PY - 2003 DA - 2003// TI - Coalescence in a Metapopulation with Recurrent Local Extinction and Recolonization JO - Evolution VL - 57 UR - https://doi.org/10.1111/j.0014-3820.2003.tb00307.x DO - 10.1111/j.0014-3820.2003.tb00307.x ID - Pannell2003 ER - TY - JOUR AU - Duffy, S. AU - Shackelton, L. A. AU - Holmes, E. C. PY - 2008 DA - 2008// TI - Rates of evolutionary change in viruses: patterns and determinants JO - Nat Rev Genet VL - 9 UR - https://doi.org/10.1038/nrg2323 DO - 10.1038/nrg2323 ID - Duffy2008 ER - TY - JOUR AU - Mikalsen, A. B. AU - Sindre, H. AU - Mjaaland, S. AU - Rimstad, E. PY - 2005 DA - 2005// TI - Expression, antigenicity and studies on cell receptor binding of the hemagglutinin of infectious salmon anemia virus JO - Arch Virol VL - 150 UR - https://doi.org/10.1007/s00705-005-0502-4 DO - 10.1007/s00705-005-0502-4 ID - Mikalsen2005 ER - TY - JOUR AU - Kibenge, F. S. AU - Kibenge, M. J. AU - Wang, Y. AU - Qian, B. AU - Hariharan, S. AU - McGeachy, S. PY - 2007 DA - 2007// TI - Mapping of putative virulence motifs on infectious salmon anemia virus surface glycoprotein genes JO - J Gen Virol VL - 88 UR - https://doi.org/10.1099/vir.0.83097-0 DO - 10.1099/vir.0.83097-0 ID - Kibenge2007 ER - TY - JOUR AU - Gouy, M. AU - Guindon, S. AU - Gascuel, O. PY - 2010 DA - 2010// TI - SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building JO - Mol Biol Evol VL - 27 UR - https://doi.org/10.1093/molbev/msp259 DO - 10.1093/molbev/msp259 ID - Gouy2010 ER - TY - JOUR AU - Katoh, K. AU - Kuma, K. AU - Toh, H. AU - Miyata, T. PY - 2005 DA - 2005// TI - MAFFT version 5: improvement in accuracy of multiple sequence alignment JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki198 DO - 10.1093/nar/gki198 ID - Katoh2005 ER - TY - JOUR AU - Watterson, G. A. PY - 1975 DA - 1975// TI - On the number of segregating sites in genetical models without recombination JO - Theor Popul Biol VL - 7 UR - https://doi.org/10.1016/0040-5809(75)90020-9 DO - 10.1016/0040-5809(75)90020-9 ID - Watterson1975 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 - TY - JOUR AU - Kuhner, M. K. AU - Yamato, J. AU - Felsenstein, J. PY - 1995 DA - 1995// TI - Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling JO - Genetics VL - 140 ID - Kuhner1995 ER - TY - JOUR AU - Kuhner, M. K. PY - 2006 DA - 2006// TI - LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btk051 DO - 10.1093/bioinformatics/btk051 ID - Kuhner2006 ER - TY - JOUR AU - Posada, D. AU - Crandall, K. A. PY - 2001 DA - 2001// TI - Evaluation of methods for detecting recombination from DNA sequences: Computer simulations JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.241370698 DO - 10.1073/pnas.241370698 ID - Posada2001 ER - TY - JOUR AU - Kosakovsky Pond, S. L. AU - Posada, D. AU - Gravenor, M. B. AU - Woelk, C. H. AU - Frost, S. D. PY - 2006 DA - 2006// TI - GARD: a genetic algorithm for recombination detection JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl474 DO - 10.1093/bioinformatics/btl474 ID - Kosakovsky Pond2006 ER - TY - JOUR AU - Delport, W. AU - Poon, A. F. Y. AU - Frost, S. D. W. AU - Kosakovsky Pond, S. L. PY - 2010 DA - 2010// TI - Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq429 DO - 10.1093/bioinformatics/btq429 ID - Delport2010 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 - Drummond, A. J. AU - Rambaut, A. PY - 2007 DA - 2007// TI - BEAST: Bayesian evolutionary analysis by sampling trees JO - BMC Evol Biol VL - 7 UR - https://doi.org/10.1186/1471-2148-7-214 DO - 10.1186/1471-2148-7-214 ID - Drummond2007 ER - TY - JOUR AU - Suchard, M. A. AU - Weiss, R. E. AU - Sinsheimer, J. S. PY - 2001 DA - 2001// TI - Bayesian Selection of Continuous-Time Markov Chain Evolutionary Models JO - J Mol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003872 DO - 10.1093/oxfordjournals.molbev.a003872 ID - Suchard2001 ER - TY - JOUR AU - Parker, J. AU - Rambaut, A. AU - Pybus, O. G. PY - 2008 DA - 2008// TI - Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty JO - Infect Genet Evol VL - 8 UR - https://doi.org/10.1016/j.meegid.2007.08.001 DO - 10.1016/j.meegid.2007.08.001 ID - Parker2008 ER - TY - STD TI - Lemey P, Rambaut A, Drummond AJ, Suchard MA: Bayesian Phylogeography Finds Its Roots. PLoS Comput Biol. 2009, 5 (9): ID - ref64 ER - TY - JOUR AU - Kosakovsky Pond, S. L. AU - Frost, S. D. W. 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. W. AU - Muse, S. V. PY - 2004 DA - 2004// TI - HyPhy: hypothesis testing using phylogenies JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti079 DO - 10.1093/bioinformatics/bti079 ID - Kosakovsky Pond2004 ER - TY - JOUR AU - Sali, A. AU - Blundell, T. L. PY - 1993 DA - 1993// TI - Comparative Protein Modelling by Satisfaction of Spatial Restraints JO - J Mol Biol VL - 234 UR - https://doi.org/10.1006/jmbi.1993.1626 DO - 10.1006/jmbi.1993.1626 ID - Sali1993 ER - TY - JOUR AU - Thompson, J. D. AU - Higgins, D. G. AU - Gibson, T. J. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - JOUR AU - Jones, D. T. PY - 1999 DA - 1999// TI - Protein secondary structure prediction based on position-specific scoring matrices JO - J Mol Biol VL - 292 UR - https://doi.org/10.1006/jmbi.1999.3091 DO - 10.1006/jmbi.1999.3091 ID - Jones1999 ER - TY - JOUR AU - Brooks, B. R. AU - Bruccoleri, R. E. AU - Olafson, B. D. AU - States, D. J. AU - Swaminathan, S. AU - Karplus, M. PY - 1983 DA - 1983// TI - CHARMM: A program for macromolecular energy, minimization, and dynamics calculations JO - J Comput Chem VL - 4 UR - https://doi.org/10.1002/jcc.540040211 DO - 10.1002/jcc.540040211 ID - Brooks1983 ER - TY - JOUR AU - Phillips, J. C. AU - Braun, R. AU - Wang, W. AU - Gumbart, J. AU - Tajkhorshid, E. AU - Villa, E. AU - Chipot, C. AU - Skeel, R. D. AU - Kalé, L. AU - Schulten, K. PY - 2005 DA - 2005// TI - Scalable molecular dynamics with NAMD JO - J Comput Chem VL - 26 UR - https://doi.org/10.1002/jcc.20289 DO - 10.1002/jcc.20289 ID - Phillips2005 ER - TY - JOUR AU - Guex, N. AU - Peitsch, M. C. PY - 1997 DA - 1997// TI - SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling JO - Electrophoresis VL - 18 UR - https://doi.org/10.1002/elps.1150181505 DO - 10.1002/elps.1150181505 ID - Guex1997 ER -