@article{Perez-Losada2015,
author = {P{\'{e}}rez-Losada, Marcos and Arenas, Miguel and Gal{\'{a}}n, Juan Carlos and Palero, Ferran and Gonz{\'{a}}lez-Candelas, Fernando},
doi = {10.1016/j.meegid.2014.12.022},
journal = {Infection, Genetics and Evolution},
number = {December},
pages = {296--307},
title = {{Recombination in viruses: Mechanisms, methods of study, and evolutionary consequences}},
volume = {30},
year = {2015}
}

@article{Lole1999,
author = {Lole, K S and Bollinger, R C and Paranjape, R S and Gadkari, D and Kulkarni, S S and Novak, N G and Ingersoll, R and Sheppard, H W and Ray, S C},
journal = {Journal of virology},
number = {1},
pages = {152--60},
pmid = {9847317},
title = {{Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.}},
volume = {73},
year = {1999}
}

@article{Etherington2005a,
author = {Etherington, Graham J. and Dicks, Jo and Roberts, Ian N.},
doi = {10.1093/bioinformatics/bth500},
journal = {Bioinformatics},
number = {3},
pages = {278--281},
pmid = {15333462},
title = {{Recombination Analysis Tool (RAT): A program for the high-throughput detection of recombination}},
volume = {21},
year = {2005}
}

@article{Martin2015,
author = {Martin, Darren P. and Murrell, Ben and Golden, Michael and Khoosal, Arjun and Muhire, Brejnev},
doi = {10.1093/ve/vev003},
journal = {Virus Evolution},
number = {1},
pages = {1--5},
title = {{RDP4: Detection and analysis of recombination patterns in virus genomes}},
volume = {1},
year = {2015}
}

@article{Liitsola2000a,
author = {Liitsola, Kirsi and Holm, Kirsi and Bobkov, Aleksei and Pokrovsky, Vadim and Smolskaya, Tatjana and Leinikki, Pauli and Osmanov, Saladin and Salminen, Mika},
doi = {10.1089/08892220050075309},
journal = {AIDS Research and Human Retroviruses},
number = {11},
pages = {1047--1053},
title = {{An AB recombinant and its parental HIV type 1 strains in the area of the former Soviet Union: Low requirements for sequence identity in recombination}},
volume = {16},
year = {2000}
}

@article{Smith2014,
author = {Smith, Donald B. and Bukh, Jens and Kuiken, Carla and Muerhoff, A. Scott and Rice, Charles M. and Stapleton, Jack T. and Simmonds, Peter},
doi = {10.1002/hep.26744},
journal = {Hepatology},
number = {1},
pages = {318--327},
pmid = {24115039},
title = {{Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: Updated criteria and genotype assignment web resource}},
volume = {59},
year = {2014}
}

@article{Jiang1999,
author = {Jiang, X. and Espul, C. and Zhong, W. M. and Cuello, H. and Matson, D. O.},
doi = {10.1007/s007050050651},
journal = {Archives of Virology},
number = {12},
pages = {2377--2387},
title = {{Characterization of a novel human calicivirus that may be a naturally occurring recombinant}},
volume = {144},
year = {1999}
}

@article{Sprygin2018,
  doi = {10.1371/journal.pone.0207480},
  url = {https://doi.org/10.1371/journal.pone.0207480},
  year  = {2018},
  publisher = {PLOS},
  volume = {13},
  number = {12},
  pages = {1--19},
  author = {Alexander Sprygin, Yurii Babin, Yana Pestova, Svetlana Kononova, David B. Wallace, Antoinette Van Schalkwyk, Olga Byadovskaya, Vyacheslav Diev, Dmitry Lozovoy, Alexander Kononov},
  title = {Analysis and insights into recombination signals in lumpy skin disease virus recovered in the field},
  journal = {PLoS ONE}
}

@article{Larkin2007,
author = {Larkin, M. A. and Blackshields, G. and Brown, N. P. and Chenna, R. and Mcgettigan, P. A. and McWilliam, H. and Valentin, F. and Wallace, I. M. and Wilm, A. and Lopez, R. and Thompson, J. D. and Gibson, T. J. and Higgins, D. G.},
doi = {10.1093/bioinformatics/btm404},
journal = {Bioinformatics},
number = {21},
pages = {2947--2948},
pmid = {17846036},
title = {{Clustal W and Clustal X version 2.0}},
volume = {23},
year = {2007}
}

@article{Katoh2002,
author = {Katoh, K.},
doi = {10.1093/nar/gkf436},
journal = {Nucleic Acids Research},
number = {14},
pages = {3059--3066},
pmid = {12136088},
title = {{MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform}},
volume = {30},
year = {2002}
}

@article{Okonechnikov2012,
author = {Okonechnikov, Konstantin and Golosova, Olga and Fursov, Mikhail and Varlamov, Alexey and Vaskin, Yuri and Efremov, Ivan and {German Grehov}, O. G. and Kandrov, Denis and Rasputin, Kirill and Syabro, Maxim and Tleukenov, Timur},
doi = {10.1093/bioinformatics/bts091},
journal = {Bioinformatics},
number = {8},
pages = {1166--1167},
title = {{Unipro UGENE: A unified bioinformatics toolkit}},
volume = {28},
year = {2012}
}
