Haploview

Haploview is a handy tool for haplotype analysis, which helps in molecular genetic testing to spot DNA segments that have similarities. This software was designed to make these tasks easier and more efficient.

Easy to Use and Cross-Platform

This app is built on Java, so it works on different platforms without needing any installation. That means you can jump right in without any hassle!

Simplicity at Its Best

The interface is straightforward and user-friendly. You can load up to five file formats: standard linkage, data dumps from the HapMap Project, PHASE, or PLINK. Plus, if you’ve got a bunch of files, you can use the “-batch” command line to load them all at once.

Customizable Parameters for Better Analysis

No matter what file format you choose to load into Haploview, you'll find that the same parameters can be adjusted. You can compare markers pairwise based on a value you set (the default is 500KB).

Excluding Missing Genotypes

If there are individuals with missing genotypes, you can set a value to exclude them from your analysis. This makes your results more accurate!

Advanced Configuration Options

If you're using standard linkage files, there are extra settings available. You can enable association testing or work with family trio data, making it flexible for your specific needs.

Diverse Display Options

After loading your file, Haploview offers various displays like LD plots, haplotypes, check markers, or tagger options that mix pairwise methods with multi-marker approaches.

Online Features with PHASE Format

If you're working with PHASE format and have an Internet connection, you can download the HapMap info track directly within the app.

A Multi-Purpose Tool for Everyone

This program isn't just about running LD and haplotype analysis; it's also great for estimating haplotype frequency in populations! It even supports permutation testing to help find significant associations.

User-Friendly for All Levels!

Haploview is perfect for students who are getting into this field and it's flexible enough for anyone looking to dive deeper into haplotype analysis tasks.