{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,4,22]],"date-time":"2023-04-22T17:54:55Z","timestamp":1682186095429},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,7,15]]},"abstract":"Abstract<\/jats:title>\n Summary: 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.<\/jats:p>\n Availability and implementation: 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 .<\/jats:p>\n Contact: \u00a0mal@chinaaids.cn or yshao08@gmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu154","type":"journal-article","created":{"date-parts":[[2014,3,29]],"date-time":"2014-03-29T01:45:49Z","timestamp":1396057549000},"page":"2073-2075","source":"Crossref","is-referenced-by-count":8,"title":["CorMut: an R\/Bioconductor package for computing correlated mutations based on selection pressure"],"prefix":"10.1093","volume":"30","author":[{"given":"Zhenpeng","family":"Li","sequence":"first","affiliation":[{"name":"1 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 2 Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China"}]},{"given":"Yang","family":"Huang","sequence":"additional","affiliation":[{"name":"1 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 2 Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China"}]},{"given":"Yabo","family":"Ouyang","sequence":"additional","affiliation":[{"name":"1 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 2 Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China"}]},{"given":"Yang","family":"Jiao","sequence":"additional","affiliation":[{"name":"1 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 2 Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China"}]},{"given":"Hui","family":"Xing","sequence":"additional","affiliation":[{"name":"1 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 2 Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China"}]},{"given":"Lingjie","family":"Liao","sequence":"additional","affiliation":[{"name":"1 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 2 Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China"}]},{"given":"Shibo","family":"Jiang","sequence":"additional","affiliation":[{"name":"1 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 2 Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China"}]},{"given":"Yiming","family":"Shao","sequence":"additional","affiliation":[{"name":"1 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 2 Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China"}]},{"given":"Liying","family":"Ma","sequence":"additional","affiliation":[{"name":"1 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 2 Key Laboratory of Medical Molecular Virology (Ministries of Education and Health), Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai 200032, China"}]}],"member":"286","published-online":{"date-parts":[[2014,3,28]]},"reference":[{"key":"2023012711252387500_btu154-B1","doi-asserted-by":"crossref","first-page":"3722","DOI":"10.1128\/JVI.78.7.3722-3732.2004","article-title":"Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase","volume":"78","author":"Chen","year":"2004","journal-title":"J. Virol."},{"key":"2023012711252387500_btu154-B2","volume-title":"Elements of Information Theory","author":"Cover","year":"2012"},{"key":"2023012711252387500_btu154-B3","doi-asserted-by":"crossref","first-page":"3312","DOI":"10.1093\/bioinformatics\/btm515","article-title":"Co-evolving residues in membrane proteins","volume":"23","author":"Fuchs","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012711252387500_btu154-B4","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1016\/S0168-9525(02)02722-1","article-title":"The Ka\/Ks ratio: diagnosing the form of sequence evolution","volume":"18","author":"Hurst","year":"2002","journal-title":"Trends Genet."},{"key":"2023012711252387500_btu154-B5","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1093\/protein\/gzs081","article-title":"Reliable and robust detection of coevolving protein residues","volume":"25","author":"Jeong","year":"2012","journal-title":"Protein Eng. Des. 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