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Whole Genome Alignment

The Whole Genome Alignment plugin to the QIAGEN CLC Genomics Workbench delivers tools supporting the investigation of evolutionary relationships through multiple genome alignment and comparison, including interactive exploration and visualization.

The functionality can be used to work with small to medium sized genomes (up to 100M base pairs) and includes:

  • Aligning multiple genomes
  • Visualizing large-scale events, such as inversions and translocations
  • Fast generation and flexible display of whole genome dot plots
  • Calculating the Average Nucleotide Identity
  • Creating evolutionary trees and heat maps based on the average nucleotide identity
  • Importing and exporting standard whole genome alignments formats (MAF and XMFA)
  • Extracting multiple sequence alignments (based on annotations, e.g. only coding regions)
  • Transfer annotations from a selected reference genome to other sequences in the alignment

 

Figure 1. Screenshot of an interactive whole genome alignment view of multiple Salmonella genomes produced by the Whole Genome Alignment plugin.

Check out this blog with performance benchmarks of this plugin.

Latest Improvements

We frequently release updates and improvements such as bug fixes or new features. To get a complete overview, please visit the latest improvements page.

Downloads

Plugin Manual
Online manual Download manual
Plugin Download
Download plugin
Download Whole Genome Alignment (Beta)

Version

Platform support

Download

20.1.0

QIAGEN CLC Genomics Workbench


 [20.0.4, 20.0.3, 20.0.2, 20.0.1, 20.0]

QIAGEN CLC Main Workbench


 [20.0.4, 20.0.3, 20.0.2, 20.0.1, 20.0]

1.0.0 Beta v.1

QIAGEN CLC Genomics Workbench


 [12.0.4, 12.0.3, 12.0.2, 12.0.1, 12.0]

QIAGEN CLC Main Workbench


 [8.1.4, 8.1.3, 8.1.2, 8.1.1, 8.1]
Server Plugin Download
Download plugin
Download Whole Genome Alignment Server Plugin (Beta)

Version

Platform support

Download

20.1.0

QIAGEN CLC Genomics Server


 [20.0.4, 20.0.3, 20.0.2, 20.0.1, 20.0]

1.0.0 Beta v.1

QIAGEN CLC Genomics Server


 [11.0.4, 11.0.3, 11.0.2, 11.0.1, 11.0]

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