AB1 file viewer plus chromatogram evidence
Open AB1 files against the expected construct and jump to the bases that need a decision.
AB1 VIEWER + VALIDATION
AB1 viewer, FASTQ validation, and repeatable protein multiple sequence alignment
Open AB1 files, review chromatograms, check FASTQ-backed calls, and rerun AlignCove protein MSA with the same output every time.
OUTCOMES
Two alignment stories, one evidence trail
FASTQ viewer for read-supported calls
See how much support each FASTQ mismatch has before you decide whether it is real.
QC notes stay attached to the construct
Keep validation outcomes, comments, and follow-up history with the same construct record.
Get the same protein multiple sequence alignment every time
Repeatable MSA matters when you compare variants across experiments or need a stable methods story.
SEQUENCING VALIDATION
AB1 viewer and sequencing validation
Open AB1 files and ABI traces against the expected construct
Use RayCrest as Sanger sequence analysis software with construct-aware mismatch review and coding-impact context from the start.
- Import verified Sanger trace formats:
.ab1and.abi. - Automatic mismatch detection against the expected sequence.
- Coding-impact visibility while reviewing calls.
Chromatogram viewer for mismatch evidence
Move from a flagged mismatch to review chromatograms and supporting evidence without switching tools.
- Step through mismatches one by one or filter to the ones that affect coding sequence.
- See the reference sequence, read, and quality score side by side.
- Add notes while you are looking at the evidence, not later when the context is gone.
QC history stays attached to the construct
Compare multiple runs against one construct, resolve disagreements, and keep the decision history where teammates can find it.
- Conflict and coverage cues across the full sequence span.
- Fast jump to the first unresolved mismatch across runs.
- QC summaries preserved with construct history.
FASTQ viewer for read-supported calls
When a base looks off, the built-in FASTQ viewer keeps read support and QC context at the exact position under review.
- See how many reads support each flagged base. One read is suspicious; twenty is convincing.
- Spot patterns that suggest sequencing noise versus a real mutation.
- Mark each call as pass or fail and attach a note so the decision stays with the evidence.
MULTIPLE SEQUENCE ALIGNMENT
Protein multiple sequence alignment with AlignCove
Reruns you can compare — not just reruns
Most teams don't need just any alignment result. They need one they can rerun later and still compare directly against earlier decisions, figures, and methods.
- Same input leads to the same protein multiple sequence alignment output.
- Pipeline behavior stays fixed instead of shifting between runs.
- Diagnostics stay attached for review and methods support.
Alignment viewer, tree view, and diagnostics in one workflow
AlignCove is RayCrest’s built-in protein alignment tool, so you can inspect the alignment itself, switch to the tree view, and keep run diagnostics nearby.
- Inspect aligned positions without exporting into another alignment app.
- Switch to the tree view when you need relationship context across sequences.
- Keep MSA runs close to plasmid and validation workflows in the same Mac workspace.
TECHNICAL DETAILS
Validation inputs and deeper AlignCove detail
What the AB1, ABI, and FASTQ validation workflows accept
The validation story is centered on evidence-linked review, not just on a final pass or fail label.
- Verified Sanger trace inputs:
.ab1and.abi. - Verified FASTQ inputs:
.fastq,.fq, and.fastq.gz. - QC notes, mismatch decisions, and history stay attached to the construct under review.
AlignCove pipeline stages (high level)
AlignCove uses a multi-stage process tuned for difficult protein families, especially the distantly related ones where standard tools often produce shaky alignments.
- Input normalization and QA checks
- Difficulty statistics (count, length, and similarity profile)
- Guide-tree construction from k-mer distances (k=6)
- Progressive alignment (sequence-sequence, sequence-profile, and profile-profile with affine-gap DP)
- Pairwise rescue candidate evaluation only in final two-sequence merge cases
- Stage-3 bounded local refinement with deterministic tie-breaks
- Final output plus run diagnostics metadata
Preset behavior, rescue constraints, and determinism caveat
The preset behavior is locked down so repeated runs stay comparable, and the rescue step is constrained rather than open-ended.
AlignCoveV1 is the stable shipping preset. Today, aligncove and aligncove-v1 produce identical results for the same input (with remote7 retained as a historical alias).
When the workflow reaches a final two-sequence merge, a small deterministic rescue set may be evaluated (for example, diagonal-biased DP and terminal-gap rebalance). Rescue is accepted only if the unbiased score improves and safety checks pass.
No ML inference is used in this pipeline; behavior is algorithmic and deterministic.
OXBench benchmark snapshot (quality-only)
AlignCove performs comparably to established tools like T-Coffee and MAFFT on difficult protein families, landing within about 7% of the best-per-family score while also giving reproducible output on repeat runs.
On a curated set of 13 difficult OXBench families (SP-F1, higher is better):
- AlignCoveV1 mean SP-F1: 0.6337
- Best external tool per family (mean SP-F1): 0.7053
- Gap to best-per-family mean: 0.0715
External tool mean SP-F1 on the same set: T-Coffee 0.6758, ProbCons 0.6620, MUSCLE 0.6587, MAFFT 0.6572, Clustal Omega 0.6511, MSAProbs 0.5822.
This comparison is quality-only and does not include external runtime measurements.
Alignment viewer and tree views
Once the run finishes, you can inspect the alignment itself or switch to a tree view without exporting the data into another tool first.
WORKFLOW + OUTPUTS
From trace import to saved decision
Typical workflow
-
Import
Add Sanger
.ab1/.abitraces or FASTQ runs and attach them to the expected construct. -
Review
Navigate mismatch calls, inspect chromatogram or FASTQ support, and confirm evidence at read/base resolution.
-
Decide
Mark the construct as passed, flagged, or failed so the decision and the evidence behind it stay saved together.
Outputs
- Evidence-linked alignment review records per run
- Mismatch and QC decision history tied to construct revisions
- Shareable QC export artifacts for notebooks and collaborators
- Deterministic MSA outputs with run diagnostics
RELATED NEXT STEPS
Go deeper on validation and MSA
AB1 Viewer
See the dedicated Sanger and AB1 workflow page
Use the focused landing page when you need the AB1 file viewer, chromatogram viewer, and construct-linked validation story in one place.
MSA
See the dedicated multiple sequence alignment page
Get the plain-English AlignCove story, plus viewer, tree view, and determinism messaging tuned for protein MSA searches.
Access
Request beta access for validation workflows
Tell us if AB1 review, FASTQ-backed decisions, or repeatable protein MSA is the workflow your team needs first.
Construct Editing
Return to the plasmid editor when the sequence needs work
Move from evidence review back into the construct workspace for edits, primer redesign, and the next cloning pass.
Review sequencing evidence and run repeatable protein MSA from one Mac app
Beta access is free. We review every request within 24 hours.