植物叶绿体密码子偏好RSCU聚类

1.提取cds编码序列
略
2.计算密码子偏好性
用EMBOSS的cusp计算

cusp -sequence R6517.cds -outfile R6517.codon.freq
#CdsCount: 53

#Coding GC 37.91%
#1st letter GC 46.19%
#2nd letter GC 38.10%
#3rd letter GC 29.44%

#Codon AA Fraction Frequency Number
GCA    A     0.280    15.577    333
GCC    A     0.168     9.309    199

3.聚类
参考（https://www.cnblogs.com/foreverycc/archive/2013/04/19/3029873.html）
整理数据成表

head coden_RSCU.tab
Codon   KT220690        KT220692        MCB     NC027259        NC029370        NC035143        NC035233        NC037247
GCA     1.1197  1.1163  1.1193  1.1053  1.1234  1.1047  1.1212  1.1050
GCC     .6273   .6239   .6521   .6571   .6230   .6452   .6700   .7050
GCG     .4856   .4856   .4436   .4953   .5004   .4695   .4646   .4610
GCT     1.7672  1.7740  1.7848  1.7422  1.7531  1.7804  1.7441  1.7288
TGC     .4705   .4705   .4913   .5361   .5263   .4588   .4869   .4608
TGT     1.5294  1.5294  1.5086  1.4638  1.4736  1.5411  1.5130  1.5391
GAC     .3952   .3971   .3901   .3962   .3888   .3887   .3948   .4155
GAT     1.6047  1.6028  1.6098  1.6037  1.6111  1.6112  1.6051  1.5844
GAA     1.5342  1.5360  1.5512  1.5275  1.5257  1.5459  1.5375  1.5326

使用pvClust包聚类

library(pvclust)
a<-read.table(coden_RSCU.tab,header=T)
b<-a[,2:9]
fit <- pvclust(b, method.hclust="ward",method.dist="euclidean")
plot(fit, cex = .5)

图片.png