How To Construct Phylogenetic Tree Using Snps
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11.1 years ago
Zhu ▴ 100

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 .

snp phylogenetics • 22k views
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11.1 years ago

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

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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!

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

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11.1 years ago
Ahdf-Lell-Kocks ★ 1.6k

I would try Margarita:

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

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11.1 years ago

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

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

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What format is your data in?

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

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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

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