Question: How To Construct Phylogenetic Tree Using Snps
5
gravatar for Zhu
7.5 years ago by
Zhu80
Zhu80 wrote:

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 .

phylogenetics snp • 15k views
ADD COMMENTlink modified 4.6 years ago by Biostar ♦♦ 20 • written 7.5 years ago by Zhu80
3
gravatar for Caddymob
7.5 years ago by
Caddymob950
United States
Caddymob950 wrote:

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

ADD COMMENTlink written 7.5 years ago by Caddymob950

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!

ADD REPLYlink written 7.5 years ago by Zhu80

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

ADD REPLYlink written 7.5 years ago by Caddymob950
2
gravatar for Ahdf-Lell-Kocks
7.5 years ago by
Ahdf-Lell-Kocks1.6k
Ahdf-Lell-Kocks1.6k wrote:

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.

ADD COMMENTlink written 7.5 years ago by Ahdf-Lell-Kocks1.6k
0
gravatar for Zev.Kronenberg
7.5 years ago by
United States
Zev.Kronenberg11k wrote:

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

 

ADD COMMENTlink modified 3.9 years ago • written 7.5 years ago by Zev.Kronenberg11k

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

ADD REPLYlink written 7.5 years ago by Zhu80

What format is your data in?

ADD REPLYlink written 7.5 years ago by Zev.Kronenberg11k

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

ADD REPLYlink written 6.0 years ago by sarah0

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

ADD REPLYlink written 3.9 years ago by sunilthorat20

please see my updated post.

ADD REPLYlink written 3.9 years ago by Zev.Kronenberg11k
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