Comparison view

seqhiker can compare multiple genomes in a stacked view with pairwise matches drawn between neighboring genomes.

Opening comparison view

  • Click the view-switch button in the top toolbar to switch from the browser to Comparison view.

  • With comparison view open:

    • drag genome files into the window one-by-one

    • or use the download button to fetch genomes directly into the comparison stack

When no genomes are loaded, the view shows an empty-state prompt.

Loading genomes

Comparison mode accepts the same sequence and annotation sources as browser mode:

  • FASTA

  • GenBank

  • EMBL

  • GFF3 with embedded sequence

  • FASTA plus companion GFF3

If you drop a sequence file together with its matching GFF3, the comparison genome is loaded with annotations.

A standalone GFF3 with embedded ##FASTA can also be loaded directly as one comparison genome.

Layout

Each genome row shows:

  • forward-strand annotations

  • a contig map strip

  • nucleotide letters when zoomed in enough

  • coordinate axis

  • reverse-strand annotations

Matches are drawn only between neighboring genomes in the stack.

Core interactions

  • Drag the “up/down arrow” button to reorder genomes.

  • Use the lock buttons between rows to lock or unlock neighboring genomes.

  • Locked genomes pan together.

  • Double-click a match to align that match near the left side of the visible window.

  • Click a match to select it and open details in the right panel.

  • Click empty space to clear the selected match.

Region selection

Click and drag across a genome row to select a region.

That:

  • highlights the selected interval on that genome

  • opens a selected matches panel on the right

  • lists overlapping matches to the genome above and/or below

Selecting a result in that panel focuses the corresponding match in the main view.

Search and Go

In comparison mode:

  • Search includes a genome dropdown

  • Go includes both a genome dropdown and a chromosome/contig dropdown

Search results include the matching genome name. Go ranges also adjust the comparison zoom when a range is entered.

Zoomed-in detail

At high zoom, comparison mode shows:

  • nucleotide letters

  • per-base alignment connectors

  • sine-wave SNP connectors in a contrasting theme color

Indels appear as non-parallel lines in the alignment.

Saving and loading sessions

Comparison mode can save the current comparison session to a custom file. These files can be dropped back into the app later to restore the comparison genomes.

Temporary view slots

Comparison mode has its own temporary view slots, separate from browser mode:

  • Shift+1 to Shift+9 save slots

  • 1 to 9 load slots

The saved state includes:

  • row order

  • per-genome offsets

  • current zoom span

Export

The screenshot button exports the current comparison viewport as SVG.

Only the currently visible comparison content is exported, and match geometry is clipped to the visible window.