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How To Generate Phylogeny Tree, Based On Snps?

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.

snp phylogeny
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updated by Bioch'Ti • Bioch'Ti • written by Naren Naren

1 answer

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.

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written by Bioch'Ti • Bioch'Ti

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

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written by Naren Naren

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

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written by Bioch'Ti • Bioch'Ti

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?

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written by Adrian Pelin Adrian Pelin

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