I have a large multiple nucleotide alignment, and I need to delete specific nucleotide positions from each sequence (basically I need to delete several columns of nucleotides). Someone familiar with a sufficient way to do this?
I was thinking to read an alignment as data.frame in R, and then delete selected columns. But I am having troubles to separate nucleotides by columns.
what I have now:
mydata<-readDNAStringSet("myalignmet.fas") names<-names(mydata) sequence<-paste(mydata) ptid<-names df<-data.frame(names, sequence) df$sequence<-as.character(df$sequence) df2$sequence<-strsplit(df2$sequence, " ")
I am getting a column df$sequence as c("A", "C", "G", "T", ...).
Thanks in advance, Maria