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vimalinx

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1. ▌
   Window Maker · vimalinx bundle

   Use when you need to create adjacent or sliding windows across a genome or BED file for binning genomic regions into fixed-size or fixed-count intervals.
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2. ▌
   Windowmasker · vimalinx bundle

   Use when masking repetitive or low-complexity regions in genomic sequences before alignment or database searches
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3. ▌
   Xtract Linux · vimalinx bundle

   Use when calling the Linux-specific compiled `xtract.Linux` binary directly to extract tabular or XML output from structured XML records.
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4. ▌
   Align Columns · vimalinx bundle

   Use when pretty-printing tab-delimited output with left, center, right, or decimal-aware numeric alignment in EDirect text workflows.
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5. ▌
   Analyse Dists · vimalinx bundle

   Use when passing legacy ViennaRNA distance-matrix data through the AnalyseDists helper for simple formatting or downstream plotting workflows.
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6. ▌
   Archive Nmcds · vimalinx bundle

   Use when building or refreshing a local RefSeq NM CDS archive for offline accession and coding-sequence lookups.
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7. ▌
   Bed12 To Bed6 · vimalinx bundle

   Use when you need to explode BED12 transcript or block annotations into one BED6 interval per block, such as converting multi-exon records into simple exon intervals for downstream interval analysis.
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8. ▌
   Bowtie2 Build · vimalinx bundle

   Use when building Bowtie 2 index files from reference FASTA sequences for subsequent read alignment with bowtie2.
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9. ▌
   Bowtie2sam Pl · vimalinx bundle

   Use when converting legacy Bowtie text output into SAM and retaining only the best alignment per read.
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10. ▌
    Color Chrs Pl · vimalinx bundle

    Use when rendering `bcftools +color-chrs` `.dat` output into an SVG chromosome-coloring plot, optionally with custom haplotype colors.
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11. ▌
    Esl Compalign · vimalinx bundle

    Use when comparing a test multiple sequence alignment against a trusted reference alignment to compute accuracy. Requires Stockholm format files with
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12. ▌
    Esl Construct · vimalinx bundle

    Use when inspecting, comparing, or rebuilding consensus RNA/DNA secondary-structure annotation in Stockholm alignments.
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13. ▌
    Esl Mixdchlet · vimalinx bundle

    Use when fitting, scoring, generating, or sampling mixture Dirichlet priors for count-vector data used in HMMER or Infernal-style models.
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14. ▌
    Esl Translate · vimalinx bundle

    Use when translating nucleotide sequences to amino acid sequences using Easel's translation utility from the HMMER suite.
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15. ▌
    Export2sam Pl · vimalinx bundle

    Use when converting legacy Illumina GERALD export files into SAM for downstream alignment analysis.
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16. ▌
    Filter Record · vimalinx bundle

    Use when filtering records from Entrez/NCBI data streams as part of entrez-direct workflows.
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17. ▌
    Fuse Segments · vimalinx bundle

    Use when you need to merge simple tabular start/end segments into non-overlapping intervals inside EDirect-style pipelines.
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18. ▌
    Hmmpgmd Shard · vimalinx bundle

    Use when running the sharded `hmmpgmd_shard` daemon so large protein sequence databases are split across HMMER worker nodes.
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19. ▌
    Intersect Bed · vimalinx bundle

    Use when you need to find overlaps between two genomic interval files (BED, GFF, VCF, or BAM), filter features by intersection, or count/report overlapping regions between datasets.
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20. ▌
    Just Top Hits · vimalinx bundle

    Use when keeping only the first N query groups from a first-column-grouped tabular hit table.
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21. ▌
    Makeprofiledb · vimalinx bundle

    Use when creating PSSM databases for rpsblast, cobalt, or deltablast searches. Formats position-specific scoring matrices into BLAST-compatible profile databases.
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22. ▌
    Maq2sam Short · vimalinx bundle

    Use when converting legacy MAQ short-map files into SAM for downstream SAMtools-compatible processing.
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23. ▌
    Multi Bam Cov · vimalinx bundle

    Use when you need to count read coverage from multiple BAM files across specific genomic regions defined in a BED, GFF, or VCF file.
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24. ▌
    Plot Bamstats · vimalinx bundle

    Use when visualizing `samtools stats` output as BAM QC plots, including merged reports and reference-GC-aware summaries.
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25. ▌
    Plot Vcfstats · vimalinx bundle

    Use when converting `bcftools stats` output into variant-QC plots, per-sample PNG panels, and optional PDF summaries.
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26. ▌
    Print Columns · vimalinx bundle

    Use when projecting or transforming tab-delimited stdin columns with a tiny EDirect `awk` wrapper, especially for quick field arithmetic, quoting, or date stamping in shell pipelines.
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27. ▌
    Refseq Nm Cds · vimalinx bundle

    Use when retrieving RefSeq NM coding sequences for supported species (cow, frog, human, mouse, pig, rat, zebrafish) via the entrez-direct toolkit.
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28. ▌
    Run With Lock · vimalinx bundle

    Use when wrapping a command in NCBI-style file locking so only one worker for a given lock base runs at a time.
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29. ▌
    Starlong Avx2 · vimalinx bundle

    Use when aligning long RNA-seq reads to a reference genome using the AVX2-optimized STARlong aligner for splice-aware mapping.
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30. ▌
    Starlong Sse3 · vimalinx bundle

    Use when aligning long RNA-seq reads to a reference genome using STARlong with SSE3 optimization, or when generating genome indices for long-read splice-aware alignment.
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31. ▌
    Subread Align · vimalinx bundle

    Use when aligning RNA-seq or genomic DNA-seq reads to a reference index. Supports paired-end and single-end reads in FASTQ, FASTA, SAM, or BAM formats.
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32. ▌
    Vcf Consensus · vimalinx bundle

    Use when applying VCF variants to a reference FASTA to generate a consensus sequence.
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33. ▌
    Vcf Validator · vimalinx bundle

    Use when you need to validate VCF files for format compliance and detect issues like duplicate positions.
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34. ▌
    Wgsim Eval Pl · vimalinx bundle

    Use when evaluating wgsim simulation results or analyzing simulated read data as part of samtools bioconda installations.
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35. ▌
    Accn At A Time · vimalinx bundle

    Use when splitting mixed accession-like text into one lowercase token per line in EDirect-style text pipelines.
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36. ▌
    Archive Nihocc · vimalinx bundle

    Use when maintaining a local NIH Open Citation Collection archive for offline citation-link lookups in EDirect workflows.
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37. ▌
    Archive Nlmnlp · vimalinx bundle

    Use when maintaining a local NLM NLP concept archive over PubMed for offline chemical, disease, gene, or GeneRIF lookups.
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38. ▌
    Archive Pubmed · vimalinx bundle

    Use when maintaining a local PubMed XML archive for offline literature search, indexing, or bulk processing.
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39. ▌
    Complement Bed · vimalinx bundle

    Use when you need to find genomic regions NOT covered by features in a BED/GFF/VCF file, such as identifying gaps, intergenic regions, or uncovered intervals.
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40. ▌
    Esl Compstruct · vimalinx bundle

    Use when comparing two Stockholm format files with secondary structure markup to evaluate how well a test structure matches a trusted reference.
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41. ▌
    Expand Current · vimalinx bundle

    Use when expanding and rebuilding the local EDirect PubMed `Current` archive plus its derived index layers.
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42. ▌
    Fasta From Bed · vimalinx bundle

    Use when extracting DNA or RNA sequences from a FASTA file using coordinate ranges from BED, GFF, or VCF files.
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43. ▌
    Feature Counts · vimalinx bundle

    Use when you need to assign aligned sequencing reads to genes or genomic features for expression quantification from SAM/BAM files
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44. ▌
    Filter Columns · vimalinx bundle

    Use when filtering or manipulating columns in tabular data files from bioinformatics workflows.
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45. ▌
    Filter Genbank · vimalinx bundle

    Use when filtering or processing GenBank-format sequence records retrieved via NCBI Entrez Direct tools
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46. ▌
    Hisat2 Align L · vimalinx bundle

    Use when aligning RNA-seq reads to a reference genome using a HISAT2 index, particularly for splice-aware alignment of transcriptomic data.
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47. ▌
    Hisat2 Align S · vimalinx bundle

    Use when aligning RNA-seq reads to a HISAT2 index using the alignment binary directly. Supports spliced alignment with optional splice site annotation.
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48. ▌
    Hisat2 Build L · vimalinx bundle

    Use when building large HISAT2 index files from reference sequences for RNA-seq alignment with splice-aware mapping support.
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49. ▌
    Hisat2 Build S · vimalinx bundle

    Use when building a HISAT2 graph-based index from reference sequences for splice-aware RNA-seq alignment, optionally incorporating SNPs, haplotypes, splice sites, or exon annotations.
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50. ▌
    Hisat2 Inspect · vimalinx bundle

    Use when you need to inspect HISAT2 index files, extract reference sequences, view index summaries, or retrieve SNP/splice site/exon information from a .ht2 index.
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51. ▌
    Pair At A Time · vimalinx bundle

    Use when turning a plain-text stream into adjacent lowercase word pairs for EDirect-style text mining, token-neighbor extraction, or lightweight bigram generation.
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52. ▌
    Quality Scores · vimalinx bundle

    Use when sampling per-base Phred quality values from FASTQ, gzipped FASTQ, BAM, or SAM files via the Subread `qualityScores` utility.
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53. ▌
    Sort By Length · vimalinx bundle

    Use when sorting plain text lines by character length, especially in shell pipelines where one logical item is stored per line.
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54. ▌
    Starlong Plain · vimalinx bundle

    Use when aligning long RNA-seq reads (PacBio, Nanopore) to a reference genome using splice-aware mapping with STARlong.
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55. ▌
    Starlong Ssse3 · vimalinx bundle

    Use when aligning long RNA-seq reads to a reference genome with splice-aware mapping using the SSSE3-optimized STARlong binary.
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56. ▌
    Test Pmc Index · vimalinx bundle

    Use when validating a local PMC archive/index configured through `EDIRECT_LOCAL_ARCHIVE` by round-tripping random PMC records through `xfetch` and `xsearch`.
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57. ▌
    Vcf Fix Ploidy · vimalinx bundle

    Use when VCF files have incorrect ploidy annotations for sex chromosomes or mitochondrial DNA, particularly when processing samples with known sex but mismatched genotype fields.
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58. ▌
    Vrfs Variances · vimalinx bundle

    Use when summarizing `bcftools +vrfs`/`vrfs` `SITE` output into selected sites or variance vectors from a subset of loci.
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59. ▌
    Word At A Time · vimalinx bundle

    Use when tokenizing free text into lowercase one-word-per-line output by stripping non-alphanumeric separators.
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60. ▌
    Yeast Database · vimalinx

    Use when working inside the local `yeast_genome_learning` project to download, validate, and analyze Saccharomyces cerevisiae reference data through its teaching scripts.
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61. ▌
    Blast Formatter · vimalinx bundle

    Use when you need to reformat BLAST archive files into different output formats (tabular, HTML, custom) without re-running the BLAST search.
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62. ▌
    Bowtie2 Align L · vimalinx bundle

    Use when aligning sequencing reads to a reference using Bowtie 2's large-index alignment engine.
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63. ▌
    Bowtie2 Align S · vimalinx bundle

    Use when aligning sequencing reads (FASTQ/FASTA) to a reference genome using Bowtie 2. Supports paired-end, unpaired, interleaved, and BAM inputs with SAM output.
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64. ▌
    Bowtie2 Build L · vimalinx bundle

    Use when building large Bowtie 2 index files from reference sequences for alignment of reads to large genomes (>4 billion bases).
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65. ▌
    Bowtie2 Build S · vimalinx bundle

    Use when building Bowtie 2 index files from reference sequences for short-read alignment.
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66. ▌
    Bowtie2 Inspect · vimalinx bundle

    Use when you need to extract reference sequences, names, or summary information from a Bowtie2 index file.
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67. ▌
    Download Pubmed · vimalinx bundle

    Use when you need to bulk-download PubMed baseline or update files from NCBI's FTP server for local offline analysis.
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68. ▌
    Guess Ploidy Py · vimalinx bundle

    Use when plotting `bcftools +guess-ploidy -v` output into a PNG summary of haploid, diploid, score, and site-count signals across samples.
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69. ▌
    Legacy Blast Pl · vimalinx bundle

    Use when converting NCBI C toolkit BLAST command lines to NCBI C++ toolkit equivalents.
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70. ▌
    Reorder Columns · vimalinx bundle

    Use when you need to reorder columns in tabular bioinformatics data files while preserving row content.
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71. ▌
    Rnaseq Pipeline · vimalinx

    Use when building or reviewing an end-to-end RNA-seq workflow from raw reads through quantification, differential expression, and basic interpretation.
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72. ▌
    Sort Uniq Count · vimalinx bundle

    Use when counting nonblank text lines after an internal sort, especially when you want case-insensitive grouping in a compact shell wrapper.
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73. ▌
    Split At Intron · vimalinx bundle

    Use when processing genomic sequences that require splitting at intron boundaries as part of Entrez Direct workflows.
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74. ▌
    Starlong Sse4 1 · vimalinx bundle

    Use when aligning long RNA-seq reads to a reference genome or generating genome indexes for spliced transcript alignment
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75. ▌
    Transmute Linux · vimalinx bundle

    Use when calling the Linux-specific compiled `transmute.Linux` binary directly for NCBI format conversion, sequence processing, or variation-processing workflows.
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76. ▌
    Vcf Indel Stats · vimalinx bundle

    Use when calculating in-frame indel ratios from VCF files, optionally with exon annotations.
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77. ▌
    Vcf Phased Join · vimalinx bundle

    Use when joining multiple overlapping pre-phased VCF chunks into a single phased VCF using heterozygous calls from overlaps to determine correct phase.
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78. ▌
    Archive Taxonomy · vimalinx bundle

    Use when maintaining a local NCBI Taxonomy archive for offline lineage and taxon lookups in EDirect workflows.
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79. ▌
    Extract Exons Py · vimalinx bundle

    Use when extracting exon coordinates from GTF annotation files for HISAT2 index building or transcriptome analysis.
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80. ▌
    Gen Random Reads · vimalinx bundle

    Use when simulating transcriptome reads from a transcript FASTA and TPM table with `genRandomReads`, or when summarizing transcript lengths before building that TPM table.
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81. ▌
    Hisat2 Inspect L · vimalinx bundle

    Use when you need to inspect or extract information from HISAT2 large index files (.ht2l), including reference sequences, splice sites, SNPs, exons, or index summaries.
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82. ▌
    Hisat2 Inspect S · vimalinx bundle

    Use when extracting metadata, reference names, SNPs, splice sites, or exon information from HISAT2 index files (.ht2).
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83. ▌
    Subread Fullscan · vimalinx bundle

    Use when scanning a reference index for all high-similarity genomic locations of one specific read sequence string.
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84. ▌
    Union Bed Graphs · vimalinx bundle

    Use when you need to align multiple bedGraph tracks onto a shared interval segmentation so their values can be compared side by side.
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85. ▌
    Vcf Fix Newlines · vimalinx bundle

    Use when VCF files have inconsistent or non-native newline characters and need normalization before downstream processing.
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86. ▌
    Vcf Shuffle Cols · vimalinx bundle

    Use when you need to reorder sample columns in a VCF file to match the column order of a template VCF.
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87. ▌
    Between Two Genes · vimalinx bundle

    Use when extracting the inclusive tabular block between two gene-name rows from a first-column gene list or interval table.
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88. ▌
    Blastdb Aliastool · vimalinx bundle

    Use when creating BLAST database aliases, converting GI files to binary format, or aggregating multiple BLAST databases into a single virtual database.
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89. ▌
    Bowtie2 Inspect L · vimalinx bundle

    Use when you need to inspect or extract information from a Bowtie 2 large index (.bt2l) file, including reference sequence names, lengths, or FASTA sequences.
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90. ▌
    Bowtie2 Inspect S · vimalinx bundle

    Use when you need to inspect Bowtie 2 index files to extract reference sequence names, lengths, or index summary information from .bt2 files.
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91. ▌
    Combine Uid Lists · vimalinx bundle

    Use when unioning multiple Entrez or NCBI UID files into one deduplicated numeric-sorted list.
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92. ▌
    Convert2blastmask · vimalinx bundle

    Use when converting lower-case masked FASTA files to masking formats compatible with makeblastdb for BLAST database preparation.
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93. ▌
    Download Flatfile · vimalinx bundle

    Use when mirroring consolidated NCBI GenBank flatfile divisions into the current directory or verifying existing downloaded flatfiles.
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94. ▌
    Download Sequence · vimalinx bundle

    Use when downloading NCBI ASN.1 biological sequence archive divisions such as BCT, PLN, or VRL into the current directory.
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95. ▌
    Exclude Uid Lists · vimalinx bundle

    Use when subtracting one Entrez or NCBI UID file from another and keeping only IDs unique to the first file.
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96. ▌
    Fasta Sanitize Pl · vimalinx bundle

    Use when sanitizing FASTA or FASTQ record names so they conform to SAM-compatible reference / read-name character rules.
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97. ▌
    Filter Stop Words · vimalinx bundle

    Use when processing text or queries in Entrez workflows to remove common stop words from input streams
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98. ▌
    Protein Structure · vimalinx

    Use when planning or staging protein-structure prediction or structure-design work in this workspace, especially when deciding between missing local predictors and the repos that are actually present.
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99. ▌
    Sequence Analysis · vimalinx

    Use when routing DNA, RNA, or protein sequence tasks to the core sequence-analysis commands that are actually installed in this workspace.
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100. ▌
     Test Pubmed Index · vimalinx bundle

     Use when validating a local PubMed archive/postings installation configured through `EDIRECT_LOCAL_ARCHIVE` and related local EDirect helpers.
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