Biological Sequence & Alignment Viewer

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---
name: biological-sequence-viewer
description: Open, inspect, analyze, safely edit copies of, and export local biological sequences and alignments in Codex's interactive workbench. Use for FASTA/FASTQ, GenBank/EMBL, MSA formats, ABIF/SCF chromatograms, SnapGene DNA, annotations, variants, or regional read evidence.
---

# Biological Sequence & Alignment Viewer

Use this skill when a user wants to inspect local biological sequences, alignments, annotated constructs or sequencing traces visually inside Codex. For detailed UI-to-agent mappings, binary compatibility or comparisons with specialist viewers, consult the [capability matrix](../../CAPABILITY_MATRIX.md); do not claim exhaustive Jalview, IGV, SnapGene, Benchling or FastQC parity.

## Opening Workflow

The plugin contributes native file-pane preview and a model-visible inline MCP App for supported sequence and alignment files. The model should not read or copy file bytes into the conversation merely to open the viewer.

For user-provided local files:

1. Resolve the user's intended records and requested view or analysis. Prefer explicitly named paths. If the request is ambiguous, search only the relevant workspace and ask a short clarification question when multiple plausible artifacts remain. Residue-by-residue comparisons across FASTAs, including substitutions, indels, or conservation, need an alignment; comparing lengths, GC, or QC does not.
2. Confirm that the file is a supported biological sequence or alignment artifact. For an alignment comparison, prefer opening the completed, verified alignment over the raw sequence collection. When preparing a new alignment from source records, preserve source files and record identities, record the actual producer and parameters, and verify the expected rows, common column width, and preservation of each source sequence after removing alignment gaps. Separate source files can first be assembled into one derived collection using authorized workspace tools. Combining records or observing equal lengths does not establish an alignment; do not force unaligned records into Alignment mode or rename raw FASTA to an alignment suffix.
3. Call `sequence.open_from_chat` with the exact absolute local path whenever available. Omit `presentation` for the default `"full"` viewer; pass `presentation: "inline"` only when the user or onboarding flow explicitly requests minimal controls. The persistent **Show controls** header action restores controls in both Sequence and Alignment modes; the header and **More actions** remain available when controls are hidden. A workspace-relative path works only when the MCP host exposes active roots. The tool opens the rich app inline beneath its tool-call row and returns a `viewerSessionId` in `structuredContent`; use that ID immediately for same-turn `sequence.control_viewer` calls instead of waiting for later model context.
4. For an alignment comparison starting from raw records in a mounted collection, query `records` through `sequence.query_viewer` as needed for exact IDs, then call `sequence.align`. A started job is not a completed alignment: follow its status while available and confirm that the same session displays the generated Alignment with the expected rows and column count. After the automatic handoff, the generated Alignment context can establish completion even if the source-side job is no longer queryable. If an authorized external workflow or fallback produces the alignment instead, open that verified output with `sequence.open_from_chat`; saving it does not change the earlier raw-record card. Complete this handoff without requiring another user prompt. If alignment or viewer control fails, report the unresolved step and distinguish independently computed results from live viewer evidence.
5. A successful open confirms session creation (`sessionReady: true`), not rendering (`viewerReady: false`). Say that the embedded viewer is opening; only say it is ready after live viewer context or an 

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