Dear All
I have about 60 SNPs and there positions(from NCBI) in the excel. I also have the a 500 sample with haplotype for each in nex. I'd like to get the genetic distance per base pair between each two in order. Is there any tools I can use? For example, one certain R package? what format of input files do I need? like fasta?
While, I'm a green hand and i don't know where to start. For example, what format to input and what to output.
Thank you so much.
DnaSP is a pretty easy to use program that can calculate several useful statistics including pairwise comparisons. It can use a nexus (.nex) as an input file.
http://www.ub.edu/dnasp/
You can always use a PC emulator to run PC programs on a Mac. A colleague of main teaches a genetics class where they use a Mac all semester but run some PC only programs (including DnaSP) on the Mac using Virtualbox, which is fairly easy to use and install. Below is a link to an Apple forum about PC emulators.
https://discussions.apple.com/docs/DOC-2741
- Badges
- Science method