Building phylogeny from 1000 Genome VCF file for 2504 individuals, also including ancient and primate genomes.
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README.md
VCFtoTree.py

README.md

The latest version is here:

https://github.com/duoduoo/VCFtoTree_3.0.0

VCFtoTree

Build phylogeny from [1000 Genomes] Phase 3 VCF file for 2504 individuals, also including ancient ([Neanderthal], [Denisovan]) and primate genomes. [1000 Genomes]:http://www.1000genomes.org [Neanderthal]:http://www.eva.mpg.de/neandertal/index.html [Denisovan]:http://www.eva.mpg.de/denisova/index.html

VCF --> fasta sequence (whole sequence, not just variable sites) --> Phylogeny

We provide a user friendly interface, in which you can choose the genomes you want to add into the phylogeny.

Raw scripts can be found in Code folder.

Availability and requirement

VCFtoTree was designed for Mac OS users, has been tested on El Captian V10.11.5 with python 2.7.11

Here are the programs/packages needed to run the VCFtoTree.

  • For first time users, you need to make sure your Mac has install the command line tools from Apple.com
  • samtools needs to be installed in your /usr/local/bin
  • tabix needs to be installed in your /usr/local/bin
  • wget needs to be installed in your /usr/local/bin

The easiest way to check if you have those three tools, type the commands below into your Terminal:

find /usr/local/bin/tabix

find /usr/local/bin/samtools

find /usr/local/bin/wget

After making sure that you have the above three tools installed, you can download and use the app now.

The running time of the app mostly depends on 1) downloading the Neanderthal vcf file; 2) building the phylogeny using RAxML.

After the whole process finishing, the app will generate a VCFtoTree_Output folder right next to your application in which you can find the newick tree file and all other output files. (The folder will be empty before the app finishes)

On the screen there will also be message saying that "Your tree is completed."

Your tree file is the file with ".newick" extention.

APP download site:

https://www.dropbox.com/sh/sewjxmh9207fp89/AAASfUGqMBtd2_HO3CR7XA3ha?dl=0

1.0.0

The first working version of VCFtoTree.app.