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From a vcf SNP file to a phylogenetic tree

Hi everybody,

I have made a vcf file with GATK that include SNPs from 10 samples.

My goal is to make a phylogenetic tree of SNPs,

Can you redirect me toward a ressource than explain what is the possibilities from a VCF file ?.

I have imagined making a fasta file and feed it to phylogenetic inference tool such as RAxML.

Did you guys have experienced with this kind of work ?

Thanks a lot.

snp vcf phylogenetic
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updated by leeandroid leeandroid • written by Picasa Picasa

1 answer

Try http://chibba.pgml.uga.edu/snphylo/

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written by leeandroid leeandroid

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