Whole Genome Alignment 20.1
Released September 30, 2020
This is the first non-beta release of the Whole Genome Alignment plugin.
Create Whole Genome Alignment
- Rearrange contigs When enabled, the number of crossing connections between genomes is minimized by sorting, reverse complementing, and circular shifting the contigs. This provides an improved visualization of the genome alignment.
- Reference genome A reference genome can, optionally, be specified. If the Rearrange contigs option has been enabled, the input genomes will be rearranged to most closely match the specified reference genome. The reference genome itself is not modified. A view setting can then be used to color alignment blocks according to their position on the reference genome.
- Copy annotations from reference If a reference genome has been specified, annotations can be copied from the specified reference genome to the input genomes.
- Output genomes after alignment When enabled, the genomes, with any modifications made, such as contig rearrangements and added annotations, are output as sequence lists. This may be of particular interest for workflows aimed at automated annotation of genomes based on a reference genome.
Whole Genome Alignment viewer
- Color by reference position When enabled, alignment blocks will be colored according to their position on the reference genome, if one was specified when launching the Create Whole Genome Alignment tool.
- Highlight connected contigs When enabled, hovering the mouse cursor over an alignment block will dim any chromosomes or contigs that are not part of the alignment.
- Open as Sequence List in New View Available from the right-click context menu. When selected, the highlighted sequences, including any re-ordering, shifting, and reverse complement sequence, are opened in a new tab.
Fixed an issue in Create Tree from Comparison, where the trees created would appear to have bootstrap values assigned, even though this was not the case.