HelixTree Software

Powerful Analytic Tools for Population-Based Genetic Association Studies

HelixTree is the leading software application for population-based genetic association studies. Designed to overcome the ever-increasing challenges of complex candidate gene and whole genome association studies, its unique set of conventional and leading-edge analysis tools enable you to uncover more novel associations than any other program.


  • What's New
  • Overview
  • Getting Started
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SNP & Variation Suite 6.1 and 6.2: New Feature Training

SNP analysis workflow more complete with new functionality

Stratification correction using principal component analysis (enhanced “EIGENSTRAT” method) and genomic control
For most genetic models with binary or continuous traits, HelixTree now offers population stratification correction using one or both of the following methods:

Principal components as determined by PCA may also be output into a separate spreadsheet without doing association testing.

New Case/Control and Quantitative Trait Association Tests
A new Genetic Association Test window (below) offers a straightforward way of testing for genetic association against either cases vs. controls (binary traits) or quantitative traits using one or more statistical measures under any one of several genetic model assumptions. An array of additional options enables you to detect and correct for stratification using principal components analysis and genomic control, apply multiple testing corrections (including permutation testing), and output overall marker statistics, such as call rate, minor allele frequency, Hardy-Weinberg equilibrium, etc., which can be used to filter "problematic" SNPs from analysis.

Genetic association test screen shots (click to expand)
genetic association tests genetic association tests

Convert Genotypes to DD/Dd/dd
A new option has been added to the marker statistics window enabling the output of a separate spreadsheet with genotypes encoded in the DD/Dd/dd format (where the major and minor alleles are clearly identified as d and D, respectively).

What is HelixTree?

With its unique set of conventional and novel analytic tools, HelixTree provides more ways to uncover true genetic associations than any other program. It supports case/control, quantitative trait loci (QTL) and categorical type analysis including several methods for allelic, genotypic, haplotypic, copy number variation, runs of homozygosity, multi-locus, and regression-based association tests. Whether performing a small study on candidate genes or a whole genome association study with over 10,000 individuals†, HelixTree has you covered.

HelixTree offers a complete workflow for whole genome and candidate gene association analysis (click each step to see more info):


Data Import and Preparation Data Quality Control Stratification Correction Genetic Association Testing Mitigating False Positives Advanced Association Analysis

HelixTree Workflow

Explore Further

Start Accelerating Your Quest for Significance!

The following resources are available to help you get started discovering significant
SNP associations in your data:

A more complete copy number association workflow

The following processing, analysis, and quality control measures have
been added recently to make the copy number association workflow more complete:

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  • Whole Genome Association Tutorial
  • Documentation
  • Tutorials and Webinars

†See system requirements for more information.