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Miscellaneous scripts for bioinformatics that dont merit their own repo. All under MIT License unless otherwise specified.

Ks Calc

Abnormal nucleotide frequency tends to throw off normal procedures for estimating evolutionary models. A practical situation is when calculating the Ks values for the grass genes where a significant portion of them are high-GC genes (see details here). In the case of high GC genes, most of the substitutions will be either G or C, therefore the Jukes-Cantor correction will under-estimate the Ks values. The codon models in PAML, on the contrary, tend to over-estimate Ks values. The Ks calculator we want to implement here, ignores the inference of models (where it is difficult anyway, since you have very few sites to estimate the parameters in the model). Instead, we ask this: given biased substitutions, lengths, run simulations and try to fit an evolutionary model based on the simulations.

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生物信息学的其他脚本,不值得自己的回购。 除非另有说明,否则全部在MIT许可证下。

Ks Calc

核苷酸频率异常倾向于排除进化模型的正常程序。实际情况是计算草基因的Ks值时,其中很大一部分是高GC基因(详见这里)。在高GC基因的情况下,大多数取代将是G或C,因此Jukes-Cantor校正将低估Ks值。相反,PAML中的密码子模型倾向于过度估计Ks值。我们要在这里实现的Ks计算器忽略了模型的推论(无论如何还是很难,因为你有很少的站点来估计模型中的参数)。相反,我们提出这一点:给予偏置的替换,长度,运行模拟,并尝试基于模拟来适应进化模型。

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