The Whole Genome Alignment plugin makes it possible to compare genomes, and to explore and visualize their evolutionary relations (figure 1.1).
The plugin installs the tools in a Whole Genome Alignment folder in the Toolbox as seen in figure 1.2, and adds the relevant format files to the Export and Import functionality of the Workbench.
The plugin contains functionality for:
- Fast whole genome dot plots
- Aligning multiple genomes
- Visualizing alignments of multiple genomes, which can contain large-scale events such as inversions and translocations
- Calculating the Average Nucleotide Identity
- Transferring annotations from a reference genome to other genomes
- 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, optionally restricting to annotations such as coding regions
This plugin comes with certain limitations: the tools are optimized for working with small and medium-sized genomes (up to 100M bases). They are not designed for larger eukaryotic genomes.