vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Quick Start
- To use vcf2phylip import your data in VCF format.
- Resources: https://github.com/edgardomortiz/vcf2phylip
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> stacks -> test_populations_app
Input File(s)
Use glyma.Wm82.gnm1.div.Z5VC.SNPs.vcf.gz from the directory above as test input.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Default parameters only, no further configuration needed.
Output File(s)
Expect as output a series of files named after the input file:
- glyma.Wm82.gnm1.div.Z5VC.SNPs.min4.phy