title: CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure.
abstract: Correlated mutations constitute a fundamental idea in evolutionary biology, and understanding correlated mutations will, in turn, facilitate an understanding of the genetic mechanisms governing evolution. CorMut is an R package designed to compute correlated mutations in the unit of codon or amino acid mutation. Three classical methods were incorporated, and the computation results can be represented as correlation mutation networks. CorMut also enables the comparison of correlated mutations between two different evolutionary conditions.
  
  
  METHODS
  CorMut is released under the GNU General Public License within bioconductor project, and freely available at http://bioconductor.org/packages/release/bioc/html/CorMut.html.
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing 102206 and Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China.
authors.forename: Zhenpeng
authors.initials: Z
authors.lastname: Li
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing 102206 and Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Huang
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing 102206 and Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China.
authors.forename: Yabo
authors.initials: Y
authors.lastname: Ouyang
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing 102206 and Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Jiao
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing 102206 and Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Xing
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing 102206 and Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China.
authors.forename: Lingjie
authors.initials: L
authors.lastname: Liao
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing 102206 and Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China.
authors.forename: Shibo
authors.initials: S
authors.lastname: Jiang
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing 102206 and Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China.
authors.forename: Yiming
authors.initials: Y
authors.lastname: Shao
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing 102206 and Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China.
authors.forename: Liying
authors.initials: L
authors.lastname: Ma
mesh_terms: D019943:Amino Acid Substitution; D003062:Codon; D004252:DNA Mutational Analysis / Q000379:methods*; D016333:HIV Protease / Q000235:genetics; D009154:Mutation; D012984:Software
chemical_list: D003062:Codon; D016333:HIV Protease