How To Construct Phylogenetic Tree Using Snps

Question

[Zhu]

Hi, all i am strugglling to start with constructing phylogenetic tree with SNPs identified from population re-sequence data.

now i have verified SNPs with samtools and bcftools according to the mannual. but i am confused with tree constructing. may i use pseudo-genome with all sites or just SNPs concatenated sequence of each individual to construct tree?

the more details ,the better!

thanks .

Answer 1

[Caddymob]

Depends on how fancy you need to be, but I would check out the R bioconductor package snpstats. See page 16 of the LD Vignette.pdf. You'll need to convert your VCF data to ped format, you can do this easily with vcftools, I would make a tped if youf VCF is big (it will progably crash if you don't do a tped) eg:

vcftools --vcf your.vcf --plink-tped --out yourTped
plink --tfile yourTped --make-bed --out yourBed

You can also try your own hand at clustering, I gave a simple example here on biostar for ADMIXTURE data, but this is easily modified for SNPs in a tped file:Simple R clustering dendrogram

[Zhu]

thanks，i do convert vcf files to tped and bed. but what to do next? what programe should i use to construct tree with ped or bed file? would you please be more specific? thanks!

[Caddymob]

Use R... See page 16 of the LD Vignette.pdf, linked above

Answer 2

[Ahdf-Lell-Kocks]

I would try Margarita:
http://seqanswers.com/wiki/20980557

It doesn't produce trees but instead it produces ancestral recombination graphs (ARGs) which theoretically will better reflect recombination between your SNPs.

Answer 3

[Zev.Kronenberg]

If you can code -

create a binary matrix where rows are loci and columns are individuals. 1 means present 0 means not present (non reference allele).

In R use the APE package to create NJ bootstrapped trees. If your interested in more details send me a message.

UPDATE:

There are now "standard" methods for building a SNP tree. For example: http://www.biomedcentral.com/1471-2164/15/162

[Zhu]

yes, i do some perl codings. would you please give me more details about data orgnizing and converting?

[Zev.Kronenberg]

What format is your data in?

[sarah]

How do you get from the binary matrix to the NJ tree with ape?

[sunilthorat]

Dear Zev, I want to create NJ bootsrapped trees using APE, I am new to it. I have sequences in .fasta format, can you please guide me how to proceed ahead.

Sunil

[Zev.Kronenberg]

please see my updated post.