Question: From a vcf SNP file to a phylogenetic tree
1
gravatar for Picasa
2.9 years ago by
Picasa590
Picasa590 wrote:

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 phylogenetic vcf • 5.1k views
ADD COMMENTlink modified 2.9 years ago by leeandroid110 • written 2.9 years ago by Picasa590

I will link only one thread here: How To Construct Phylogenetic Tree Using Snps

If you look to the right (-->) then under similar posts you will find other similar threads.

ADD REPLYlink written 2.9 years ago by GenoMax95k
1
gravatar for leeandroid
2.9 years ago by
leeandroid110
leeandroid110 wrote:

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

ADD COMMENTlink written 2.9 years ago by leeandroid110
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