v1.1.0

• Main new feature: ntSynt-viz now outputs interactive HTML ribbon plots
  • Interactive features:
    • Hover/click on a chromosome to see the ID and length
    • Hover/click on a ribbon to outline the entire synteny block across all the genomes, and see the coordinates in each genome
    • Click on a chromosome in the colour legend to highlight all the synteny blocks mapping to that chromosome
• New parameter: --optimize-ordering
  • if specified, will optimize the top-to-bottom ordering based on minimizing total pairwise inversions, while respecting the topology of the tree/cladogram
• New output: *LLM-info.md
  • Markdown and ribbon plot image (PNG format) can be supplied to any LLM to generate a short summary of the output ribbon plot

ntSynt-viz v1.0.7

• Add option --order to specify full genome ordering top-to-bottom
• Add option --annotate-genome-info to annotate genome summary information to the right of the genomes in the ribbon plot
  • Chromosome number, genome size
• Retain all sequences in ribbon plot (longer than --seq_length), even if they are not in a synteny block

ntSynt-viz v1.0.6

• Added option --dpi to specify resolution of output ribbon plot when using --format png

ntSynt-viz v1.0.5

• Add support for visualizing pangenome graph synteny
  • Added conversion script convert_gfa_to_ntsynt_blocks.py to convert a pangenome graph in GFA format to the TSV format expected by ntSynt-viz
• Add support for SVG output
  • Output svg format by specifying --format svg
• Adjust text spacing in legend
• Fix to ribbon colour selection when there are many small (less than --seq_length) sequences in the input genomes
• Update documentation

ntSynt-viz v1.0.4

• Fixes issue where target genome was not always sorted properly to the top of the plot when part of a polytomy
• Refactored code to match tree topology to ordered leaf label list

ntSynt-viz v1.0.3

• Fixes issue when inputting rooted trees with --tree
  • Will only midpoint root a tree if it is unrooted
• If an input tree lacks branch lengths, automatically sets all branch lengths to 1

ntSynt-viz v1.0.2

• Ensures consistency between colouring of synteny blocks on full ribbon plots and ribbon plots zooming in on 1 or more chromosomes/sequences

ntSynt-viz v1.0.1

• Fix issue of ntSynt-viz stalling for some 3 genome comparisons
• Updates for ggplot 4.0.0+ compatibility
• Code refactoring

ntSynt-viz v1.0.0

Initial release of ntSynt-viz: Multi-genome synteny block visualization