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vimalinx

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1. ▌
   Update Blastdb Pl · vimalinx bundle

   Use when downloading or updating pre-formatted BLAST databases from NCBI or cloud providers (AWS, GCP)
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2. ▌
   Download Ncbi Data · vimalinx bundle

   Use when downloading static NCBI reference datasets such as taxonomy, MeSH tree, bioconcepts, generif, journals, serials, or PMC open access files via CLI.
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3. ▌
   Gatk Genotypegvcfs · vimalinx

   Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs.
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4. ▌
   Interpolate Sam Pl · vimalinx bundle

   Use when deriving interpolated per-base coverage counts from a sorted SAM file, especially across paired-end inserts.
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5. ▌
   Plot Ampliconstats · vimalinx bundle

   Use when visualizing amplicon sequencing statistics from samtools ampliconstats output, generating heatmaps and graphs for coverage and read analysis.
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6. ▌
   Run Ncbi Converter · vimalinx bundle

   Use when launching an NCBI converter binary through the `run-ncbi-converter` wrapper that downloads and caches the platform-specific executable on demand.
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7. ▌
   Subread Buildindex · vimalinx bundle

   Use when building an index from a reference sequence for Subread alignment tools.
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8. ▌
   Genome Coverage Bed · vimalinx bundle

   Use when computing genome-wide coverage from BED/GFF/VCF or BAM files, generating coverage histograms, BedGraph tracks, or per-position depth reports.
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9. ▌
   Intersect Uid Lists · vimalinx bundle

   Use when keeping only the Entrez or NCBI UIDs present in both of two UID files.
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10. ▌
    Join Into Groups Of · vimalinx bundle

    Use when batching newline-separated IDs into fixed-size comma-separated groups for EDirect calls or other list-limited APIs.
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11. ▌
    Mask Fasta From Bed · vimalinx bundle

    Use when you need to hard-mask or soft-mask regions in a FASTA file using BED, GFF, or VCF coordinates, such as repetitive elements, blacklist regions, or loci to exclude from sequence analysis.
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12. ▌
    Multi Intersect Bed · vimalinx bundle

    Use when you need to identify overlapping genomic regions across multiple BED files simultaneously.
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13. ▌
    Skip If File Exists · vimalinx bundle

    Use when filtering a newline-delimited list of file paths so only paths without an existing regular file continue downstream.
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14. ▌
    Difference Uid Lists · vimalinx bundle

    Use when finding the symmetric difference between two Entrez or NCBI UID files.
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15. ▌
    Gatk Haplotypecaller · vimalinx

    Use when running GATK HaplotypeCaller to emit per-sample germline variant calls or gVCFs from analysis-ready BAM/CRAM inputs.
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16. ▌
    Project Tree Builder · vimalinx bundle

    Use when generating or dry-running NCBI-style Unix C++ project trees with `project_tree_builder`.
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17. ▌
    Sort Uniq Count Rank · vimalinx bundle

    Use when turning repeated nonblank text lines into a frequency-ranked table, with counts sorted descending after case-insensitive grouping.
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18. ▌
    Systematic Mutations · vimalinx bundle

    Use when enumerating all single-position A/C/G/T substitutions for sequence strings inside an EDirect-style text pipeline.
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19. ▌
    Get Species Taxids Sh · vimalinx bundle

    Use when resolving taxonomy names or taxids into BLAST-filterable NCBI taxonomy IDs with the NCBI helper script.
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20. ▌
    Seq Cache Populate Pl · vimalinx bundle

    Use when populating an htslib/CRAM `REF_CACHE` directory from FASTA input or by scanning a directory tree for FASTA files.
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21. ▌
    Amino Acid Composition · vimalinx bundle

    Use when counting amino-acid letters in raw protein sequence lines inside simple EDirect text pipelines.
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22. ▌
    Bioinformatics Toolkit · vimalinx bundle

    Use when you need a workspace-level entry point to choose among the installed bioinformatics CLIs and repo-backed AI/bio projects in this environment.
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23. ▌
    Download Ncbi Software · vimalinx bundle

    Use when fetching a small set of NCBI command-line binaries (`magic-blast`, `datasets`, or `sra-toolkit`) with the bundled EDirect downloader.
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24. ▌
    Quote Grouped Elements · vimalinx bundle

    Use when converting space-separated grouped values into quoted comma-joined lines for downstream EDirect or shell formatting steps.
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25. ▌
    Extract Splice Sites Py · vimalinx bundle

    Use when extracting splice junction sites from GTF annotation files for HISAT2 genome indexing or RNA-seq alignment workflows.
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26. ▌
    Hisat2 Extract Exons Py · vimalinx bundle

    Use when extracting exon coordinates from GTF annotation files for HISAT2 index building or splice-aware alignment preparation.
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27. ▌
    Print Missing Subranges · vimalinx bundle

    Use when reporting gaps in an ordered list of ascending integer positions, identifiers, or coordinates by printing the missing ranges between observed values.
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28. ▌
    Disambiguate Nucleotides · vimalinx bundle

    Use when expanding IUPAC ambiguous nucleotide strings into all concrete DNA sequences in shell or EDirect pipelines.
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29. ▌
    Hisat2 Simulate Reads Py · vimalinx bundle

    Use when simulating RNA-seq or DNA-seq reads from a reference genome and GTF annotation file, optionally incorporating SNP variants and controlling expression profiles.
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30. ▌
    Plan Editor · vimalinx

    Use when incorporating user changes into a selected plan while preserving execution structure and validation semantics.
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31. ▌
    Run Resumer · vimalinx

    Use when resuming a paused or interrupted run from saved run state instead of regenerating the plan from scratch.
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32. ▌
    Hisat2 Read Statistics Py · vimalinx bundle

    Use when you need to compute basic read statistics (count, min/max/average length) from FASTQ/FASTA files before or after HISAT2 alignment workflows.
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33. ▌
    Skill Router · vimalinx

    Use when expanding an approved plan into stage-by-stage candidate skills drawn from the local skill registry.
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34. ▌
    Cleanup Blastdb Volumes Py · vimalinx bundle

    Use when managing BLAST database storage by removing unnecessary volume files to reclaim disk space.
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35. ▌
    Stage Reviewer · vimalinx

    Use when checking whether a completed stage produced the artifacts and validation evidence required by the approved plan.
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36. ▌
    Execution Guard · vimalinx

    Use when deciding whether a plan stage should continue automatically, pause for confirmation, or escalate because of risk.
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37. ▌
    Plan Comparator · vimalinx

    Use when comparing candidate plans and explaining trade-offs so the user can select or modify a plan.
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38. ▌
    Hisat2 Extract Splice Sites Py · vimalinx bundle

    Use when extracting splice junctions from GTF annotation files for HISAT2 splice-aware alignment.
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39. ▌
    Windowmasker 2 2 22 Adapter Py · vimalinx bundle

    Use when adapting or converting WindowMasker output files for compatibility with different BLAST pipeline versions or formats.
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40. ▌
    Request Normalizer · vimalinx

    Use when turning a natural-language biology request into a structured request object before planning.
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41. ▌
    Hisat2 Extract Snps Haplotypes Vcf Py · vimalinx bundle

    Use when extracting SNPs and haplotypes from VCF files to build variant-aware HISAT2 graph genome indexes
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42. ▌
    Candidate Plan Generator · vimalinx

    Use when generating multiple candidate plans from a normalized request before the user approves execution.
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43. ▌
    Hisat2 Extract Snps Haplotypes Ucsc Py · vimalinx bundle

    Use when extracting SNPs and haplotypes from UCSC SNP files for HISAT2 graph-based genome indexing.
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44. ▌
    Esl Mask · vimalinx bundle

    Use when applying coordinate-based masks to named sequences in FASTA or other Easel-supported sequence files.
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45. ▌
    Esummary · vimalinx bundle

    Use when fetching document summaries from NCBI Entrez databases by database name and identifier or accession
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46. ▌
    Gbf2info · vimalinx bundle

    Use when converting GenBank Flat files to structured info output for downstream parsing or analysis.
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47. ▌
    Gff Sort · vimalinx bundle

    Use when you need to reorder GFF3 records so parent features stay ahead of children in EDirect-style annotation pipelines.
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48. ▌
    Group By · vimalinx bundle

    Use when you need to summarize tabular data by grouping rows on common column values and applying aggregation operations (sum, count, mean, etc.), similar to SQL GROUP BY.
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49. ▌
    Hmmalign · vimalinx bundle

    Use when aligning sequences to a profile HMM to produce multiple sequence alignments.
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50. ▌
    Hmmbuild · vimalinx bundle

    Use when turning curated multiple-sequence alignments into profile HMM files for HMMER search or database-preparation workflows.
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51. ▌
    Hmmfetch · vimalinx bundle

    Use when you need to extract specific HMM profiles from an HMM database file by name, or index an HMM file for faster lookups.
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52. ▌
    Hmmpress · vimalinx bundle

    Use when preparing profile HMM databases for use with hmmpgmd (HMMER daemon) by creating compressed binary index files.
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53. ▌
    Json2xml · vimalinx bundle

    Use when converting JSON documents into XML for downstream EDirect or XML-based processing.
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54. ▌
    Nhmmscan · vimalinx bundle

    Use when scanning DNA or RNA sequences against a nucleotide profile HMM database such as Dfam to identify annotated families or repeated elements.
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55. ▌
    Pmc2bioc · vimalinx bundle

    Use when converting PubMed Central article XML into BioC collection XML for downstream text-mining or annotation pipelines.
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56. ▌
    Pmc2info · vimalinx bundle

    Use when converting PubMed Central article XML into normalized PMCInfo XML for local archive building or section-aware downstream parsing.
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57. ▌
    Prodigal · vimalinx bundle

    Use when predicting protein-coding genes in prokaryotic genomes or metagenomic sequences
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58. ▌
    Psiblast · vimalinx bundle

    Use when detecting distant protein homologs via iterative profile-based searches, building position-specific scoring matrices (PSSMs), or refining sequence similarity searches beyond standard BLASTP.
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59. ▌
    Ref2pmid · vimalinx bundle

    Use when converting reference citations or identifiers to PubMed IDs (PMIDs) using Entrez Direct utilities.
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60. ▌
    Rnalfold · vimalinx bundle

    Use when computing locally stable RNA secondary structures with a maximal base pair span, scanning large genomes for short RNA structures, or predicting local RNA folding with Z-score filtering.
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61. ▌
    Rnapdist · vimalinx bundle

    Use when calculating structure distances between thermodynamic ensembles of RNA secondary structures from sequence input.
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62. ▌
    Rnapvmin · vimalinx bundle

    Use when working with RNA soft constraints and need to compute pairing probabilities with position-specific perturbation minimization from the ViennaRNA package.
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63. ▌
    Rnasnoop · vimalinx bundle

    Use when searching target RNAs for interactions with a query H/ACA snoRNA, especially when the search should respect H/ACA-specific structural constraints and optionally use accessibility profiles.
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64. ▌
    Rpsblast · vimalinx bundle

    Use when searching protein sequences against conserved domain databases like CDD using reverse position-specific BLAST
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65. ▌
    Samtools · vimalinx bundle

    Use when working with SAM, BAM, or CRAM alignment files to sort, index, view, convert, or compute statistics.
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66. ▌
    Slop Bed · vimalinx bundle

    Use when you need to expand genomic intervals by adding flanking base pairs to features in BED, GFF, or VCF files.
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67. ▌
    Snp2hgvs · vimalinx bundle

    Use when converting NCBI dbSNP docsum XML into HGVS-oriented XML records for downstream variant normalization or annotation pipelines.
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68. ▌
    Sort Bed · vimalinx bundle

    Use when you need to sort BED, GFF, or VCF interval files for downstream bedtools processing, or rank records by feature size or score.
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69. ▌
    Spdi2tbl · vimalinx bundle

    Use when flattening SPDI XML records into sorted, deduplicated tabular rows for downstream variant pipelines.
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70. ▌
    Star Avx · vimalinx bundle

    Use when aligning RNA-seq reads to a reference genome with splice-aware mapping, generating genome indices, or processing single-cell RNA-seq data with STARsolo.
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71. ▌
    Starlong · vimalinx bundle

    Use when aligning long RNA-seq reads with STARlong through the CPU-dispatch wrapper installed in this environment.
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72. ▌
    Subindel · vimalinx bundle

    Use when calling short or long indels from read alignments with the Subread `subindel` tool.
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73. ▌
    Tbl2prod · vimalinx bundle

    Use when converting `spdi2tbl`-style variant rows into reference and altered product sequences for coding or protein variants.
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74. ▌
    Toml2xml · vimalinx bundle

    Use when converting TOML configuration or metadata files into XML for downstream EDirect or XML-based processing.
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75. ▌
    Vcf Isec · vimalinx bundle

    Use when you need to compute intersections, unions, or complements between bgzipped and tabix-indexed VCF or tab-delimited files.
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76. ▌
    Vcf Sort · vimalinx bundle

    Use when VCF files need sorting by chromosome and position, particularly before downstream analysis or indexing. Pipes VCF input through stdin.
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77. ▌
    Vcf Tstv · vimalinx bundle

    Use when you need to calculate the transition/transversion (Ts/Tv) ratio from VCF files for variant call quality assessment.
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78. ▌
    Vcftools · vimalinx bundle

    Use when working with Variant Call Format (VCF) files and need to filter, summarize, or manipulate variant data.
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79. ▌
    Xml2json · vimalinx bundle

    Use when converting XML documents into pretty-printed JSON for downstream parsing, provided the legacy Perl XML::Simple dependency is available.
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80. ▌
    Yaml2xml · vimalinx bundle

    Use when converting YAML documents into XML for downstream EDirect or XML-based processing.
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81. ▌
    Annot Tsv · vimalinx bundle

    Use when you need to annotate regions in a target TSV/BED file with information from overlapping regions in a source file, transfer columns between files based on genomic overlap, or filter/drop overlapping records.
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82. ▌
    Blst2tkns · vimalinx bundle

    Use when turning EDirect-style BLAST XML alignment blocks into a token stream for downstream shell or xtract-based parsing.
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83. ▌
    Bsmp2info · vimalinx bundle

    Use when converting BioSample `DocumentSummary` XML into a compact `BioSampleInfo` XML summary with accession, title, links, and harmonized attributes.
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84. ▌
    Clustalw2 · vimalinx bundle

    Use when running legacy ClustalW 2.1 multiple-sequence-alignment workflows, guide-tree calculations, or interactive alignment sessions from the command line.
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85. ▌
    Exact Snp · vimalinx bundle

    Use when calling SNPs from aligned SAM/BAM reads with Subread's `exactSNP` variant caller.
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86. ▌
    Flank Bed · vimalinx bundle

    Use when you need to create flanking intervals adjacent to BED/GFF/VCF features for promoter analysis, regulatory region discovery, or upstream/downstream sequence extraction.
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87. ▌
    Gbf2facds · vimalinx bundle

    Use when converting GenBank format files to FASTA coding sequences (CDS) for downstream sequence analysis.
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88. ▌
    Gm2ranges · vimalinx bundle

    Use when converting BLAST/genomic-map alignment summaries into compact strand-and-range tables for later interval fusion.
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89. ▌
    Hgvs2spdi · vimalinx bundle

    Use when converting EDirect HGVS XML records into NCBI SPDI XML, optionally with a precomputed accession-to-CDS-offset transform table.
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90. ▌
    Hmmsearch · vimalinx bundle

    Use when searching profile hidden Markov models against sequence databases to identify homologous sequences or protein family members
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91. ▌
    Jackhmmer · vimalinx bundle

    Use when running iterative sequence-to-sequence HMMER searches to expand a protein family from one or a few seed sequences against a sequence database.
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92. ▌
    Jsonl2xml · vimalinx bundle

    Use when converting JSON Lines streams into XML fragments for downstream EDirect or XML-based processing.
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93. ▌
    Kinwalker · vimalinx bundle

    Use when simulating RNA folding kinetics during transcription to predict cotranscriptional folding pathways and transient intermediate structures.
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94. ▌
    Links Bed · vimalinx bundle

    Use when you need to generate HTML links to UCSC Genome Browser from BED, GFF, or VCF feature files.
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95. ▌
    Merge Bed · vimalinx bundle

    Use when merging overlapping or book-ended intervals in BED/GFF/VCF files into single intervals.
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96. ▌
    Nhance Sh · vimalinx bundle

    Use when trying the `nhance.sh` shortcut wrapper around `nquire` for pathway, gene-to-pathway, LitVar, or citation-match lookups against NCBI-related endpoints.
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97. ▌
    Ref Cache · vimalinx bundle

    Use when managing local reference sequence caches for htslib-based tools. Invokes the ref-cache CLI to configure or interact with reference cache directories.
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98. ▌
    Rnacofold · vimalinx bundle

    Use when predicting secondary structures of two RNA sequences with dimerization, computing equilibrium concentrations of monomer and dimer species, or analyzing RNA-RNA hybridization thermodynamics.
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99. ▌
    Rnaduplex · vimalinx bundle

    Use when computing optimal and suboptimal secondary structures for hybridization of two RNA strands, such as probe-target binding predictions.
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100. ▌
     Rnalocmin · vimalinx bundle

     Use when analyzing RNA secondary structure landscapes to find local minima via gradient walks, generate barrier trees, or compute rates for kinetic modeling with treekin.
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