Introduction
The Whole Genome Alignment plugin enables users to compare small and medium-sized genomes (up to 100 Mb) and to explore and visualize their evolutionary relationships (figure 1.1).
Figure 1.1: A Whole Genome Alignment view.
The plugin delivers tools that are put into a Whole Genome Alignment folder under the Tools menu (figure 1.2), and adds relevant file formats to the Export and Import functionality of the Workbench.
Figure 1.2: The tools delivered by this plugin are installed in a folder called Whole Genome Alignment, under the Tools menu.
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