Review declared graphs and aligned sequence edits
Inspect expanded URDF links, prune a user-declared rooted Newick tree and trim aligned FASTA columns with complete source maps and explicit limits.
Choose the source task before editing
These tools inspect one complete local source. Use URDF for declared parent-child graph structure, Newick for an explicit taxa selection on a user-declared rooted tree, and aligned FASTA for one shared column mask across every row. A text formatter cannot establish these relationships.
Use a selected UTF-8 file or a complete paste, then keep the original with all successful downloads. Browser memory contains the input and report during processing; file content, meshes, package paths and URLs are not fetched or executed.
| Task | Input and explicit choice | Complete downloads |
|---|---|---|
| URDF | Already-expanded XML; no xacro execution | Source-bearing report.json and safe report.csv |
| Newick | Rooted tree plus keep/remove taxa JSON | Source-bearing report.json, safe report.csv and pruned.nwk |
| Aligned FASTA | Equal-width sequences; missing set and whole-column rule | Source-bearing report.json, safe report.csv and trimmed.fa |
URDF: count components and cycles, not only candidate roots
The starter has one isolated world link and a separate three-link cycle: four links, three joints, one candidate root, one cycle component and two weak components. One root alone does not make this a tree. The report includes each declaration, its resolved or unresolved references, every component and the exact UTF-8 source span.
Duplicate names or missing/repeated parent-child declarations fail atomically. Undeclared targets, multiple incoming declarations, self-loops and cycles instead produce a complete diagnosis with validDeclaredTree=false. Tree depths are supplied only when the whole declared graph is a valid tree.
Visuals, collisions, inertia, dynamics, mimic relations, joint types, meshes, model version and unknown XML remain unreviewed. Predefined and numeric XML character references are inert data. DTD/entity declarations, processing instructions, namespaced elements and xacro/substitution names are Unsupported. This result cannot certify URDF schema validity, physics or safe simulation.
Newick: preserve the original root and unknown lengths
Declare that the input is rooted, and supply a JSON array of literal taxa names. Keep mode retains the specified leaves; remove mode deletes them. Duplicate requests and unmatched names remain in the report. Underscores are literal, quoted labels support doubled quotes, and surviving internal labels and comments remain present.
For ((A:0.1,B:0.2):0.3,C:0.4):0.7; removing B and C yields (A:0.4):0.7;. The non-root unary edge uses exact decimal0.1+0.3=0.4; the original root and its0.7 root edge survive. If A has no length, the unary node is retained because its unknown length cannot be added as zero. An annotated or labeled unary node also survives.
The output is neither an MRCA extraction nor a rerooting/minimum-node search. The source nodes, retained/deleted states and contraction records remain complete. Anonymous leaves and unsupported root/profile directives reject as Unsupported. Deleting every leaf returns an error; choose at least one retained source leaf before rerunning.
Aligned FASTA: derive one complete map for every row
At90%, a column with9 missing cells among10 rows is removed, while8 among10 survives. Comparison uses integer cross multiplication, including equality. Any mode removes a column containing any selected missing symbol;0% removes every column. N and X count only when you explicitly add them to the missing set.
Every row must have equal original width. UTF-8 full headers and duplicate IDs remain distinct by row index. Supported residues are ASCII letters and *?.-. UTF-8 BOM, LF and CRLF are retained in the report’s original source and byte spans. A lone CR or an unsupported residue rejects the entire batch.
The full missingCounts and original-to-new columnMap accompany every projected row. A zero-column result is valid and produces headers with empty sequences. Downloaded FASTA uses LF. This edits an existing alignment; it does not align sequences or establish an optimal biological filter. The cited220MB dataset exceeds the10MiB budget.
Check all budgets before choosing a handoff
All limits apply together. A permitted input may still exceed the combined complete download budget; that returns no partial reports. Large text/copy is a preview, never a replacement for the complete downloads. Source text in report.json re-encodes to the original UTF-8 bytes, including a BOM when present.
| Task | Primary and structure | Combined complete downloads |
|---|---|---|
| URDF | 5MiB;10000 links;10000 joints;XML depth64 | 20MiB JSON+CSV |
| Newick | 5MiB tree+1MiB taxa JSON;50000 nodes;10000 internal levels;10000 requests;4096 UTF-16 label/number units;absolute exponent≤100 | 20MiB JSON+CSV+Newick |
| Aligned FASTA | 10MiB;10000 rows;100000 columns;8million cells;65536 UTF-16 header units;200000 physical sequence fragments | 40MiB JSON+CSV+FASTA |
- The table previews at most200 rows and2000 UTF-16 units per cell plus an ellipsis.
- Above20000 UTF-16 units, text/copy is a compact report preview with fullReportInDownload:true; download all files for full records.
- Safe CSV protects formula-looking text by default; retain original values in JSON when comparing source declarations.
- Cancel while processing, then rerun the complete source. Correct unsupported exports in the producer rather than deleting evidence to force success.
Verify the receiver’s interpretation
For URDF, trace an issue to its original byte span and inspect both the root and cyclic component. For Newick, compare original-root paths, known distance sums, unknown edge flags and annotations. For FASTA, reapply the downloaded column map to every original row and compare the complete output.
Node Worker capacity and mature-reader checks establish implementation evidence, while actual production-browser interaction and acceptance are recorded separately by the central review. This article describes the declared profile and does not convert those checks into simulator or biological conclusions.
References
- Tetrahedral robot simulation question
First-person demand: the posted model has an isolated world link and a separate three-link cycle. Only declared graph structure is reviewed here; simulator behavior is not reproduced.
- Rooted Newick species selection question
First-person demand for retaining a specified species list; a later comment explicitly says the tree is rooted. Keeping the original root is distinct from extracting an MRCA subtree.
- Whole-column FASTA gap filtering question
First-person request for whole-column filtering at at least90% gaps. The reported220MB dataset is outside this tool’s10MiB input budget.
- URDF model declarations
Correctness reference for declared links and joints, not demand evidence or a full URDF/simulation certificate.
- Newick tree format
Correctness reference. This declared profile preserves literal underscores and rejects anonymous leaves as Unsupported, without saying those variants are universally invalid.
- Biopython alignment IO
Independent-reader reference for aligned sequences; the trimming rule remains the explicitly chosen missing set and threshold.
Tools in this category
Expand a tool to see its steps, options and supported formats, then open its workspace.
URDF declared-link graph reviewInspect declared URDF links and joints for unresolved references, multiple parents, roots and cycles, preserving the full source and exact byte positions.
Explain a root-link error before opening a simulator. Review the whole declared parent-child graph, including isolated roots and separate cycles; keep the original XML beside every finding.
Steps
- Select or paste one already-expanded UTF-8 robot XML. Run the declared graph review.
- Inspect unresolved references, root count, separate components and cycle components together. Depth is available only for a valid declared tree.
- Download complete JSON/CSV and check byte locations against the original source before changing the model.
Available options
- Protect formula-like CSV text
- On by default
Capabilities and limits
- One already-expanded UTF-8 robot XML up to 5 MiB, with optional UTF-8 BOM; up to 10,000 links, 10,000 joints and XML depth 64. Complete source-containing JSON and CSV together must fit 20 MiB. All limits apply together.
- Audits declared link/joint names, parent-child references, unresolved links, multiple incoming joints, roots, strongly connected cycles, weak components and depths of a valid declared tree. A report can complete while genuine graph issues remain; one root alone is insufficient.
- Duplicate names, missing or repeated parent/child references and malformed XML reject the whole input. Unresolved declared links, self-loops, cycles and multiple parents appear as structural issues. Names are exact and case-sensitive.
- DTD/entity declarations, processing instructions, namespaced elements/xacro and unresolved ${...} or $(...) names are Unsupported. Built-in and numeric XML character references are decoded as inert names. No mesh, package, URL or external file is opened.
- Joint types, model versions, visual/collision/inertial/dynamics/mimic and unknown XML content remain unreviewed. Their original source is retained. This is not whole-URDF schema validation, physics, simulation, closed-loop repair or a claim that a robot is safe to run.
- Full JSON includes original UTF-8 source, filename/hash, all links/joints and their exact UTF-8 byte spans, each parent/child tag, components and issues. CSV contains every link/joint. Preview shows 200 rows and 2,000 UTF-16 units per cell; large reports copy only the labelled preview. Downloads remain complete.
Rooted Newick taxa pruningKeep or remove named taxa from a declared rooted Newick tree while retaining the original root, unknown edge lengths, annotations and exact decimal contractions.
Supply one rooted tree and a JSON list of exact leaf labels. Trace every kept, removed, missing or repeated request to the original tree; download the changed Newick with full provenance.
Steps
- Choose one rooted UTF-8 tree and confirm the rooted-tree declaration. Enter exact labels as a JSON array.
- Choose keep or remove; review kept/removed taxa, unmatched requests and exact edge changes.
- Download pruned Newick and full JSON/CSV. Check original-root paths and unknown-length states before using the result.
Available options
- I declare this tree rooted; retain original root
- On by default
- Request-list mode
- Keep listed taxa · Remove listed taxa
- Protect formula-like CSV text
- On by default
Capabilities and limits
- One UTF-8 single Newick tree up to 5 MiB, optional BOM, plus taxa JSON array up to 1 MiB. Up to 50,000 nodes, 10,000 internal-parenthesis depth and 10,000 requested taxa; each decoded label and numeric token up to 4,096 UTF-16 units; exponent absolute value up to 100. Complete JSON, CSV and Newick together must fit 20 MiB.
- Explicitly declare the tree rooted. Keep/remove use exact case-sensitive labels with literal underscores; quoted labels and doubled single quotes are supported. Duplicate source leaf labels are ambiguous and reject; duplicate requests and unmatched labels remain separately reported.
- The original root and its edge remain. Only an unlabeled, unannotated non-root unary node whose incoming and surviving-child lengths both exist is contracted; decimal sums are exact, including values outside float64. Missing lengths remain unknown and never become zero.
- Surviving internal labels/support and comments stay attached to their nodes. Unknown or annotated unary nodes remain. This is not MRCA extraction, re-rooting, unrooted minimum-subtree search, strict minimum-node optimization or biological inference.
- Anonymous leaves and unsupported leading directives, including [&U], are outside this profile; [&R] is retained. These restrictions do not redefine valid Newick. Removing every leaf rejects the batch; change the mode or request list to retain at least one leaf.
- Full JSON preserves original sources and hashes, all original node/length spans, every request including duplicates, kept/removed/unmatched taxa and exact contractions. CSV includes every source taxon and unmatched unique request. Preview shows 200 rows/2,000 UTF-16 units per cell; copying large reports gives only a labelled preview. Complete downloads are atomic.
Aligned FASTA whole-column trimmingRemove alignment columns using an explicit missing-character set and threshold, preserving every row, full header and complete original-to-output column map.
Apply one column decision to all equal-width sequences. Inspect missing counts and retained coordinates before downloading the projected alignment; ambiguous N/X characters count only when explicitly selected.
Steps
- Select or paste one equal-width aligned FASTA. Choose the explicit missing-character set and column rule.
- Run trimming and inspect original, retained and removed column counts. Check the complete column map when positions matter.
- Download projected FASTA and full JSON/CSV. Keep the original source and coordinates with the handoff.
Available options
- Explicit missing characters, no separator
- -
- Whole-column removal rule
- At least percentage · Any selected missing character
- Integer percentage threshold
- 90
- Protect formula-like CSV text
- On by default
Capabilities and limits
- One equal-width UTF-8 aligned FASTA up to 10 MiB, with optional BOM and LF/CRLF. Up to 10,000 rows, 100,000 source columns and 8,000,000 total residue cells; full headers up to 65,536 UTF-16 units and at most 200,000 nonempty physical sequence fragments. Complete JSON, CSV and FASTA together must fit 40 MiB.
- Residues are ASCII A–Z/a–z, *, ?, . or -. Full UTF-8 headers, duplicate IDs and source spans remain distinct. Lone CR, unsupported residues, unequal widths and control characters in headers reject; blank source lines are retained in the original text.
- Choose missing characters explicitly, then any missing value or an integer 0–100% rule. Percentage removes a column when missing count ×100 is greater than or equal to row count ×threshold. At90%,9 of10 removes and8 of10 remains; at0%, every column is removed.
- N/X ambiguity is not a gap unless you select it. This tool does not align sequences, infer relationships or choose biologically optimal trimming. The cited220MB dataset is outside the10MiB profile.
- Full JSON retains original source/hash, every full header, physical source spans, all missing counts, the complete zero-based column map and every projected sequence. CSV maps every source column; null/new empty coordinate means removed. No dense lists of millions of cause indices are silently truncated.
- Zero-column output is valid and explicit: every original header has an empty sequence. Output FASTA uses LF; original LF/CRLF/BOM remain reconstructable from report source text. Preview is200 rows/2,000 UTF-16 units per cell; large copies are labelled previews while complete downloads remain atomic.