I think this might be an easy question, but I could not solve it after reading the pegas documentation. I want to plot an haplotype network using a FASTA file and identify which mutations are separatting the distinct haplotypes.
fa <- read.FASTA("example.fa") haps <- haplotype(fa) haps50 <- subset(haps, minfreq = 50) (network <- haploNet(haps50)) plot(network, size = attr(network, "freq"),show.mutation=1,labels=T)
How can I identify the position of the mutation in my FASTA file that is separating for example haplotype
Would it be also possible to know for example, what is the haplotype sequence of one of the haplotypes? For example haplotype
V, which is quite frequent?