The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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de novo population genomics analysis

Community rating: ?????

a program to perform population genomics analysis of samples for which there is no reference genome. Samples can be in FASTQ or FASTA format. Fst, Fis, ? and expected/observed heterzygosity will be calculated.

Quick Start

Test Data


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

Input File(s)

Use indv_1.fa up to 20 at the samples for analysis box and the _Community Data -> iplantcollaborative -> example_data -> stacks_demo->_MAP.txt for the population map field

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 several files as an output. For details on what each output means please refer to the manual of the developer of stacks at

Tool Source for App

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