Can Homozygous Snps Be Used To Construct A Phylogeny?

If I have illumina sequencing for 6 isolates and I map them to a reference, I can obtain a VCF file with homozygous SNPs.

How can I use these to reconstruct a phylogeny? Is there any tool that can read VCF and feed it into a phylogenetic model?

Adrian

vcf phylogeny bowtie2

• 3,052 views • link

updated 12.8 years ago by Istvan Albert

• written 12.8 years ago by Adrian Pelin

Please check here..

Multi-sample vcf to phylogenetic tree.

How to Construct phylogenetic tree using SNPs

• 221 views • link

updated 6.6 years ago by Ram

• written 12.8 years ago by always_learning

0 answers

No answers yet.

More posts like this

SNP enrichment, how to test for it?
written 11.7 years ago by Adrian Pelin

Hello, I am comparing a couple of strains of a parasitic fungus, and the strains overall seem pretty similar, in a 3mb genome there are …
Recombination events from single end reads.
written 11.7 years ago by Adrian Pelin

Hello, I have 5 strains mixed in culture and propagated and I am trying to measure recombination rates by sequencing total DNA extracted after certain …
VCFTools: Calculation of r^2 fails
written 12.1 years ago by Adrian Pelin

Hello, I have 9 pooled population samples with variants called into a VCF files. I merged the VCF files and tried to calculate r^2, and …
Building a reference genome for pop differentiation.
written 12.2 years ago by Adrian Pelin

Hello, If I have sequenced several isolates of one species but no good reference is available, is it a good idea to try and generate …
Detect Recommbination Used Phased Vcf?
written 12.4 years ago by Adrian Pelin

Hello, I have a few clonally propagating isolate, and I called variants for each one of these isolates and managed to phase these variants for …
Newbler: Merged Miseq Reads + Mate Pairs?
written 12.4 years ago by Adrian Pelin

Hello Everyone, I recently received MiSeq 250bp PE sequencing results from a small genome (30Mb-50Mb) eukaryote, that is highly heterozygous. After doing some assemblies I …
Dating Common Ancestor
written 12.4 years ago by Adrian Pelin

Hello, I have 10 strains sequenced with NGS, and I have called polymorphisms and was able to reconstruct a phylogeny of these strains. The bad …
How To Check For Ploidy Using Ngs Only?
written 12.5 years ago by Adrian Pelin

Hello, I am working on a single celled organism, that I am isolating from a natural environment and sequencing it using illumina PE. How can …
F(St) Test? Coorelation Between Genetic Distance And Geographical Distance Between Isolates?
written 12.8 years ago by Adrian Pelin

I have a matrix in which the rows are isolates and columns are nucleotides at select sites where homozygous variation has been detected. Is there …
Snprelate And Vcf
written 12.8 years ago by Adrian Pelin

Hello, I have illumina sequencing for 6 isolates and after mapping them to a reference, I obtain a VCF file for each isolate. I have …