v0.4.0

Feature release centered on a new BLAST alignment engine with an insertion-aware alignment view and chromatogram rendering, automatic re-alignment on sequence edits, a GC content track, and a dotplot self-comparison view.

New Features

• BLAST alignment engine — a BLAST-derived engine (ported from GenePad) joins Smith-Waterman as a user-selectable alignment algorithm: multi-segment colinear HSPs align split or multi-hit reads in full, with affine-gap consolidation and a full-length fast path that guarantees the optimal solution
• Insertion-aware alignment view — read insertions (including end junk) get their own slot columns, one cell per inserted base; inserted read bases are highlighted like mismatches, small insertions no longer litter the template row with dashes, and all tracks (GC content, primer occupancy, amplimer highlight, enzyme labels) drift-map around the slots
• Automatic re-alignment — editing the template sequence re-aligns every stored alignment in the background (reads are compared in their original orientation so reverse-strand traces stay correct), and the editor shifts the old alignment model optimistically until the result arrives; the manual Re-align action is gone
• GC content track — a per-base blue–white–red gradient band below the sequence (Features → Show GC Content), with a nonlinear color curve, configurable window size in Settings, circular wraparound, and clean breaks at alignment insertion slots
• Dotplot — Diagrams → Examine Dotplot renders a k-mer canvas self-comparison of DNA/RNA sequences, coloring exact window matches green and inverted repeats purple (both can stack), with split counts and a legend
• ORF labels — ORF features get numbered names and direction arrows

Improvements

• GC content track and SnapGene history extracted into the plugin registry (can be disabled in Settings)
• Chromatogram traces draw in read order and break at the alignment's own discontinuities (missing columns, segment jumps, circular wraps), so peaks always sit on their own base cells
• Indels are left-aligned so equivalent placements no longer offset flanking matches; one insertion entry per template column
• Multi-segment and cross-origin features now round-trip as proper GenBank join locations, and order() locations parse instead of collapsing to a point
• Hovering a translated feature shows AA numbers for all overlapping translations

Bug Fixes

• Clear the selection after deletion and select inserted bases after insertion
• Full IUPAC mapping in the frontend complement tables
• Report overlapping restriction sites in the enzyme scan, and wrap circular site coordinates in MCP output
• Preserve full cross-origin primer sites in MCP export; report convert_sequence repair coordinates as 1-based
• Honor the start-codon Met convention in translation diff and refresh; normalize custom codon table frequencies; compute the 3′ mismatch flag within the 3′ anchor only
• Persist primers that have no binding sites on save
• Cap SnapGene history decompression and sequence budgets against malicious files
• Numerous alignment-view fixes: label placement past trailing insertion cells, mouse interaction in slot-widened columns, scrollbar sync by scroll ratio, scroll anchoring in template columns

Downloads

Platform	Files	Notes
macOS	.dmg, .app.tar.gz	Apple Silicon
Windows	.msi, -setup.exe (NSIS)
Linux	.flatpak	amd64 + aarch64; aarch64 verified on Fedora