Wepresentanintegratedstand-alonesoftwarepackagenamedKaKs_Calculator2.0asanupdatedversion.Itincorporates17methodsforthecalculationofnonsynonymousandsynonymoussubstitutionrates;amongthem,weaddedourmodifiedversionsofseveralwidelyusedmethodsasthegammaseriesincludingγ-NG,γ-LWL,γ-MLWL,γ-LPB,γ-MLPB,γ-YNandγ-MYN,whichhavebeendemonstratedtoperformbetterundercertainconditionsthantheiroriginalformsandarenotimplementedinthepreviousversion.Thepackageisreadilyusedfortheidentificationofpositivelyselectedsitesbasedonaslidingwindowacrossthesequencesofinterestsin5'to3'directionofprotein-codingsequences,andhaveimprovedtheoverallperformanceonsequenceanalysisforevolutionstudies.Atoolbox,includingC++andJavasourcecodeandexecutablefilesonbothWindowsandLinuxplatformstogetherwithauserinstruction,isdownloadablefromthewebsiteforacademicpurposeathttps://sourceforge.net/projects/kakscalculator2/.
