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SNPhylo

SNPhylo

Feb 03, 2021

Quick StartTo use SNPhylo, import your data in VCF, HapMap, Simple SNP or GDS format

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> SNPhylo

Input File(s)

Use Washingtonia_SNPhylo_dataset.recode.vcf 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.

  • Use these parameters within the DE app interface:

  • Maximum_PLCS: 95

  • LD_threshold: 1

  • MAF_threshold: 0.05

  • Missing_rate: 0.8

Output File(s)

Expect these files as output:

  • snphylo.output.fasta

  • snphylo.output.filtered.vcf

  • snphylo.output.gds

  • snphylo.output.id.txt

  • snphylo.output.ml.png

  • snphylo.output.ml.tree

  • snphylo.output.ml.txt

  • snphylo.output.phylip.txt

Tool Source for App