Whole Genome Alignment 25.0

Released on December 3, 2024

Improvements

• Minor improvements and bug fixes.

Whole Genome Alignment plugin 24.0

Released on January 9, 2024

Bug fixes

• Fixed an issue where Create Average Nucleotide Identity Comparison would sometimes handle overlapping annotations incorrectly. This would lead to minor deviations for the values Average Nucleotide Identity and Average Nucleotide Identity.
• Fixed an issue where Create Average Nucleotide Identity Comparison would sometimes miss aligned regions due to special circumstances of overlapping annotations.
• Fixed an issue where Extract Multiple Sequence Alignment with parameter setting “Use gap for genomes without annotations” would sometimes produce regions consisting of only gaps.

Whole Genome Alignment 23.0

Released on January 17, 2023

Updated to be compatible with CLC Genomics Workbench 23 and CLC Genomics Server 23

Whole Genome Alignment 22.0

Released on January 11, 2022

Updated to be compatible with CLC Genomics Workbench 22 and CLC Genomics Server 22.

Changes

• Fixed a bug where searching for a wrapped sequence in a circular chromosome in a whole genome alignment would select the entire chromosome.
• Added the possibility to select and open subsequences from a whole genome alignment.

Whole Genome Alignment 21.0

Released on January 12, 2021

Updated to be compatible with CLC Genomics Workbench 21 and CLC Genomics Server 21.

Whole Genome Alignment 20.1

Released September 30, 2020

This is the first non-beta release of the Whole Genome Alignment plugin.

Improvements

Create Whole Genome Alignment

New options:

• 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

New options:

• 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.

Bug fixes

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.