How To Generate Phylogeny Tree, Based On Snps?

Question

[Naren]

sample snp data:In text format

This is sample snp data:In text format
There are 28 such sequences (Only 9 shown) Numbers are nucleotide positions.
How to generate Phylogeny Tree from these snps (There are total 600000 snps).

I am using Win7.

Answer 1

[Bioch'Ti]

Hi /Vari, The best solution is to concatenate your SNP from each individual into a 'fake' sequence and then, run your phylogenetic analysis. Here is an example :http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0020340

Best, C.

[Naren]

Thanks. That gives me some clue about what should be done with my data, How will I do it, is totally my problem.

[Bioch'Ti]

If you data are organized as a matrix, a simple [R] code will solve it !

[Adrian Pelin]

Do tell :)

If I have a matrix, 6 columns, and each row shows the Nucleotide (albeit no information about positions of consecutiveness of these nucleotides), is this a reliable method of constructing trees? and can it be done by R?