简介：Theratioofnonsynonymoussubstitutionrate(Ka)tosynonymoussubstitutionrate(Ks)iswidelyusedasanindicatorofselectivepressureatsequencelevelamongdifferentspecies,anddiversemutationmodelshavebeenincorporatedintoseveralcomputingmethods.Wehavepreviouslydevelopedanewγ-MYNmethodbycapturingakeydynamicevolutiontraitofDNAnucleotidesequences,inconsiderationofvaryingmutationratesacrosssites.WenowreportafurtherimprovementofNG,LWL,MLWL,LPB,MLPB,andYNmethodsbasedonanintroductionofgammadistributiontoillustratethevariationofrawmutationrateoversites.Thenoveltycomesintwoways:(1)weincorporateanoptimalgammadistributionshapeparameteraintoγ-NG,γ-LWL,γ-MLWL,γ-LPB,γ-MLPB,andγ-YNmethods;(2)weinvestigatehowvariablesubstitutionratesaffectthemethodsthatadoptdifferentmodelsaswellastheinterplayamongfourevolutionalfeatureswithrespecttoKa/Kscomputations.Ourresultssuggestthatvariablesubstitutionratesoversitesundernegativeselectionexhibitanoppositeeffectonωestimatescomparedwiththoseunderpositiveselection.WebelievethatthesensitivityofournewmethodshasbeenimprovedthanthatoftheiroriginalmethodsunderdiverseconditionsanditisadvantageoustointroducenovelparametersforKa/Kscomputation.

简介：KaKs_Calculator是计算的一个软件包裹非同义(Ka)并且同义(K)替换通过平均的模型选择和模型评价。因为存在，为这个评价的方法采用他们的特定的变化(替换)考虑不同进化特征的模型，导致多样的估计，KaKs_Calculator在一个最大的可能性框架实现一套候选人模型并且采用Akaike信息标准测量在模型和数据之间的健康，试图包括为精确地在编码蛋白质的序列捕获进化信息需要的同样多特征。另外，为精明的Ka和K的几存在方法也被合并到这个软件。包括源代码，编译可执行文件，和文档，KaKs_Calculator为在http://evolution.genomics.org.cn/software.htm的学术使用是自由地可得到的