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vimalinx

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1. ▌
   Blastn Vdb · vimalinx bundle

   Use when searching nucleotide sequences against SRA/VDB databases using BLAST. Invokes blastn_vdb for nucleotide-nucleotide alignment with SRA accessions.
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2. ▌
   Deltablast · vimalinx bundle

   Use when performing domain-enhanced protein sequence similarity searches to detect remote homologs using conserved domain databases.
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3. ▌
   Dustmasker · vimalinx bundle

   Use when masking low-complexity regions in nucleotide sequences using the Symmetric DUST algorithm before BLAST searches or other sequence analyses.
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4. ▌
   Ecommon Sh · vimalinx bundle

   Use when auditing or reusing the shared EDirect shell functions that other Entrez Direct wrapper scripts source internally.
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5. ▌
   Esl Afetch · vimalinx bundle

   Use when retrieving specific multiple sequence alignments from an MSA file by name, or when indexing MSA files for faster access.
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6. ▌
   Esl Alimap · vimalinx bundle

   Use when comparing or mapping two multiple sequence alignments in Stockholm format to analyze their overlap or relationship.
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7. ▌
   Esl Alipid · vimalinx bundle

   Use when calculating pairwise percent identities from multiple sequence alignments in FASTA or Stockholm format.
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8. ▌
   Esl Alirev · vimalinx bundle

   Use when you need to reverse sequences in a multiple sequence alignment file. Part of the Easel toolkit distributed with HMMER.
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9. ▌
   Esl Sfetch · vimalinx bundle

   Use when you need to extract specific sequences by name from a sequence file, or index a sequence file for faster lookup.
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10. ▌
    Esl Ssdraw · vimalinx bundle

    Use when converting a Stockholm RNA or DNA alignment plus a PostScript structure template into colored secondary-structure diagrams.
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11. ▌
    Esl Weight · vimalinx bundle

    Use when adding Stockholm sequence-weight annotations to nucleotide or protein MSAs before downstream HMMER-style modeling.
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12. ▌
    Fill An Ac · vimalinx bundle

    Use when you need to populate or update AC (allele count) fields in VCF files from the vcftools suite.
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13. ▌
    Gene2range · vimalinx bundle

    Use when converting Entrez Gene `DocumentSummary` XML for one chromosome into sorted `GENE` interval XML.
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14. ▌
    Gff2gff Py · vimalinx bundle

    Use when converting GenBank-derived GFF into bcftools/csq-friendly Ensembl-like GFF3 with the legacy `gff2gff.py` helper.
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15. ▌
    Hmmconvert · vimalinx bundle

    Use when converting profile HMM files between HMMER3 ASCII or binary, legacy HMMER2, or specific 3.x text revisions.
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16. ▌
    Propmapped · vimalinx bundle

    Use when you need to calculate the proportion of mapped reads or fragments from SAM/BAM alignment files to assess mapping quality and success rates.
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17. ▌
    Psl2sam Pl · vimalinx bundle

    Use when converting UCSC PSL alignments into SAM and controlling the simple alignment score calculation.
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18. ▌
    Random Bed · vimalinx bundle

    Use when generating random genomic intervals for simulation, background sets, or statistical testing.
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19. ▌
    Remove Dup · vimalinx bundle

    Use when removing duplicate alignments from SAM or BAM files with the Subread `removeDup` CLI and a location-count cutoff.
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20. ▌
    Rna2 Dfold · vimalinx bundle

    Use when computing MFE structures, partition functions, and Boltzmann-sampled secondary structures within k,l distance neighborhoods relative to two reference structures for an RNA sequence.
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21. ▌
    Rnaalifold · vimalinx bundle

    Use when predicting consensus secondary structures from multiple sequence alignments of RNA. Computes minimum free energy structures, partition functions, and base pairing probabilities for aligned RNA sequences.
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22. ▌
    Rnainverse · vimalinx bundle

    Use when searching for RNA sequences that fold into a predefined secondary structure, inverting RNA folding predictions to find sequences matching target bracket notation structures.
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23. ▌
    Rnaparconv · vimalinx bundle

    Use when converting legacy ViennaRNA 1.8.4 energy parameter files to the 2.0+ format used by modern ViennaRNA tools.
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24. ▌
    Rpstblastn · vimalinx bundle

    Use when searching nucleotide sequences against protein domain profile databases (PSSMs) to detect conserved domains via position-specific scoring.
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25. ▌
    Run Roh Pl · vimalinx bundle

    Use when batch-running `bcftools roh` across a directory of VCF, VCF.GZ, or BCF files and merging the resulting ROH calls across samples.
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26. ▌
    Sam2vcf Pl · vimalinx bundle

    Use when converting old `samtools pileup -c` output into VCF and filtering for SNP-only or indel-only calls.
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27. ▌
    Sort Table · vimalinx bundle

    Use when sorting tab-delimited, nonblank text rows with GNU `sort` while preserving a fixed tab field separator in shell pipelines.
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28. ▌
    Star Plain · vimalinx bundle

    Use when aligning RNA-seq reads to a reference genome with splice-aware mapping, generating genome indices, or performing related operations like lift-over and BAM input processing.
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29. ▌
    Star Ssse3 · vimalinx bundle

    Use when aligning RNA-seq reads to a reference genome or generating splice-aware genome indices for transcript alignment.
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30. ▌
    Uniq Table · vimalinx bundle

    Use when removing invariant columns from a tab-delimited table, especially in EDirect or bioinformatics comparison pipelines.
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31. ▌
    Vcf Concat · vimalinx bundle

    Use when concatenating VCF files split by chromosome or when merging multiple gzipped VCFs into a single output.
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32. ▌
    Vcf Subset · vimalinx bundle

    Use when subsetting VCF files by samples or filtering variant types from bgzipped VCF input.
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33. ▌
    Vcf To Tab · vimalinx bundle

    Use when converting VCF genotype data to simple tabular format for downstream analysis or reporting.
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34. ▌
    Window Bed · vimalinx bundle

    Use when you need to find features in one file that fall within a configurable window around features in another file, including strand-aware upstream and downstream proximity searches.
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35. ▌
    Xcommon Sh · vimalinx bundle

    Use when reading or debugging the shared `xcommon.sh` shell library that supplies local-archive discovery, stdin parsing, and common helper functions to EDirect `x*` scripts.
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36. ▌
    Archive Pmc · vimalinx bundle

    Use when maintaining a local PubMed Central full-text archive for offline PMC search or bulk processing.
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37. ▌
    Closest Bed · vimalinx bundle

    Use when you need to find the closest genomic feature in one file for each feature in another file, including distance calculations and strand-aware lookups.
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38. ▌
    Cluster Bed · vimalinx bundle

    Use when you need to cluster overlapping or nearby genomic intervals in BED, GFF, or VCF files into groups.
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39. ▌
    Esl Alimask · vimalinx bundle

    Use when you need to mask columns in a multiple sequence alignment using gap frequencies, posterior probabilities, external mask files, or the RF annotation, or to truncate alignments to specific coordinate ranges.
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40. ▌
    Esl Alistat · vimalinx bundle

    Use when working with alignment files and needing statistics from HMMER's Easel toolkit.
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41. ▌
    Esl Selectn · vimalinx bundle

    Use when reservoir-sampling a fixed number of random lines from a large text file or stream without loading the whole file.
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42. ▌
    Esl Seqstat · vimalinx bundle

    Use when you need to compute and report statistics on biological sequence files (e.g., count, length distribution, composition) as part of HMMER/Easel workflows.
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43. ▌
    Esl Shuffle · vimalinx bundle

    Use when shuffling biological sequences, bootstrapping alignment columns, or generating de novo random RNA, DNA, or protein controls.
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44. ▌
    Expand Cols · vimalinx bundle

    Use when you need to expand comma-separated values in file columns into individual lines, replicating each line for every value in the specified columns.
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45. ▌
    Flatten Gtf · vimalinx bundle

    Use when you need to flatten exon-like GTF/GFF features into SAF meta-features for Subread or featureCounts workflows.
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46. ▌
    Fuse Ranges · vimalinx bundle

    Use when you need to merge overlapping or adjacent strand-specific alignment ranges encoded as comma-separated `start..end` lists in EDirect tables.
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47. ▌
    Get Overlap · vimalinx bundle

    Use when you need to append the overlap size or gap distance between two intervals that already appear on the same line, such as paired output from `bedtools window`.
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48. ▌
    Makeblastdb · vimalinx bundle

    Use when creating BLAST databases from FASTA sequence files for use with blastn, blastp, blastx, or other BLAST search tools.
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49. ▌
    Makehmmerdb · vimalinx bundle

    Use when building HMMER binary-formatted sequence databases from plain sequence files, especially for hmmpgmd-style serving or specialized accelerated workflows.
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50. ▌
    Makembindex · vimalinx bundle

    Use when you need to create a BLAST database index for faster search operations on BLAST databases.
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51. ▌
    Md5sum Lite · vimalinx bundle

    Use when computing plain MD5 digests for files or stdin in lightweight HTSlib-based workflows without GNU md5sum features.
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52. ▌
    Novo2sam Pl · vimalinx bundle

    Use when converting legacy Novoalign text output into SAM, especially for unique alignments and optional paired-end interpretation.
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53. ▌
    Pair To Bed · vimalinx bundle

    Use when you need to find overlaps between paired-end read intervals (BEDPE or BAM) and genomic features in BED, GFF, or VCF format.
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54. ▌
    Plot Roh Py · vimalinx bundle

    Use when plotting runs of homozygosity from `run-roh.pl` style output directories into PNG tracks, optionally filtered by region, sample list, or group contrast.
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55. ▌
    Rfdiffusion · vimalinx

    Use when working from the local RFdiffusion repository to generate protein backbones or binder designs through its Docker Compose workflows.
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56. ▌
    Rnadistance · vimalinx bundle

    Use when calculating distances between RNA secondary structures, including base pair distance and tree or string editing-based dissimilarity measures.
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57. ▌
    Rnaforester · vimalinx bundle

    Use when comparing, aligning, or computing similarity/distance between RNA secondary structures, or when generating multiple structure alignments with consensus prediction.
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58. ▌
    Rnalalifold · vimalinx bundle

    Use when predicting locally stable secondary structures from multiple sequence alignments of RNA
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59. ▌
    Samtools Pl · vimalinx bundle

    Use when working with samtools.pl, a Perl CLI utility installed by the bioconda samtools package.
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60. ▌
    Shuffle Bed · vimalinx bundle

    Use when you need to randomly permute feature locations across a genome for statistical testing or generating null distributions.
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61. ▌
    Soap2sam Pl · vimalinx bundle

    Use when converting legacy SOAP aligner text output into SAM, including paired-end interpretation with `-p`.
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62. ▌
    Star Sse4 1 · vimalinx bundle

    Use when aligning RNA-seq reads to a reference genome, generating STAR genome indices, or performing splice-aware transcript alignment.
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63. ▌
    Tblastn Vdb · vimalinx bundle

    Use when searching protein queries against translated SRA or WGS-backed VDB databases with BLAST.
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64. ▌
    Test Eutils · vimalinx bundle

    Use when probing NCBI E-utilities reachability or endpoint health with the bundled `-alive`, `-all`, or per-endpoint diagnostic checks.
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65. ▌
    Vcf Compare · vimalinx bundle

    Use when comparing two or more bgzipped and tabix-indexed VCF files to assess concordance of variant calls, positions, or genotypes.
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66. ▌
    Vcf Convert · vimalinx bundle

    Use when converting VCF files between format versions (4.0, 4.1, 4.2) for compatibility with downstream bioinformatics tools.
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67. ▌
    Vcfutils Pl · vimalinx bundle

    Use when working with VCF file utilities from the bcftools bioconda package.
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68. ▌
    Xa2multi Pl · vimalinx bundle

    Use when expanding BWA `XA:Z` alternate-alignment tags in SAM records into separate secondary SAM alignments for downstream tools.
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69. ▌
    Zoom2sam Pl · vimalinx bundle

    Use when converting legacy Zoom aligner output into SAM and the read length must be supplied explicitly.
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70. ▌
    Analyse Seqs · vimalinx bundle

    Use when analyzing equal-length sequence sets with the legacy ViennaRNA statistical-geometry, clustering, or distance-matrix utility driven from stdin.
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71. ▌
    Annotate Bed · vimalinx bundle

    Use when you need to annotate BED/GFF/VCF intervals with coverage depth and breadth from multiple feature files.
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72. ▌
    Archive Pids · vimalinx bundle

    Use when maintaining a local PubMed-to-PMCID postings archive for offline identifier crosswalks in EDirect workflows.
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73. ▌
    Bam To Fastq · vimalinx bundle

    Use when converting BAM alignment files to FASTQ format, including paired-end data requiring separate or interleaved output.
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74. ▌
    Bedpe To Bam · vimalinx bundle

    Use when converting BEDPE (or BED/GFF/VCF) feature records to BAM format for downstream analysis.
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75. ▌
    Blast2sam Pl · vimalinx bundle

    Use when converting legacy plain-text blastn output into SAM records for downstream SAM/BAM-compatible tooling.
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76. ▌
    Blastdbcheck · vimalinx bundle

    Use when verifying integrity and validity of BLAST databases before using them in search pipelines or troubleshooting database corruption issues.
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77. ▌
    Coverage Bed · vimalinx bundle

    Use when computing coverage depth and breadth of features from one interval file overlapping intervals in another. Applies to BED, GFF, or VCF inputs requiring overlap counts, covered bases, and coverage fractions.
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78. ▌
    Download Pmc · vimalinx bundle

    Use when bulk-downloading PubMed Central OA tarballs across the standard PMC sections with the EDirect helper script.
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79. ▌
    Esl Alimanip · vimalinx bundle

    Use when manipulating multiple sequence alignment files using Easel tools from HMMER.
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80. ▌
    Esl Alimerge · vimalinx bundle

    Use when merging multiple sequence alignment files in Stockholm or Pfam format into a single alignment.
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81. ▌
    Esl Histplot · vimalinx bundle

    Use when turning one numeric value per line into Easel or xmgrace histogram or survival-plot data for score-distribution analysis.
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82. ▌
    Esl Reformat · vimalinx bundle

    Use when you need to convert sequence files between different formats such as FASTA, Stockholm, A2M, Clustal, or Phylip.
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83. ▌
    Esl Seqrange · vimalinx bundle

    Use when splitting an SSI-indexed sequence file into per-process sequence-index ranges for embarrassingly parallel Easel or HMMER jobs.
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84. ▌
    Fasterq Dump · vimalinx bundle

    Use when extracting FASTQ or FASTA files from NCBI SRA run accessions, especially after staging runs locally with prefetch.
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85. ▌
    Fill Ref Md5 · vimalinx bundle

    Use when VCF headers need reference and contig tags with MD5 checksums per VCFv4.1 specification.
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86. ▌
    Find In Gene · vimalinx bundle

    Use when filtering EDirect `GENE` XML records by strand and coordinate overlap to emit matching gene names.
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87. ▌
    Hisat2 Build · vimalinx bundle

    Use when building HISAT2 index files from reference genomes for subsequent alignment with hisat2. Handles FASTA reference inputs and creates .ht2 index files.
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88. ▌
    Maq2sam Long · vimalinx bundle

    Use when converting legacy MAQ long-map files into SAM for downstream SAMtools-compatible processing.
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89. ▌
    Pair To Pair · vimalinx bundle

    Use when comparing two paired-end BEDPE files to find overlapping pairs. Requires -a and -b BEDPE input files.
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90. ▌
    Phage Design · vimalinx

    Use when working from the local Evo 2 `phage_gen` project to design or analyze bacteriophage genomes, competition assays, or Gibson assembly fragments.
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91. ▌
    Qualfa2fq Pl · vimalinx bundle

    Use when merging a legacy FASTA file and matching QUAL file into FASTQ, including `.gz` inputs, before downstream alignment or QC steps.
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92. ▌
    Rchive Linux · vimalinx bundle

    Use when calling the Linux-specific compiled `rchive.Linux` binary directly to build, query, or manage local XML archives and postings indices.
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93. ▌
    Rnaaliduplex · vimalinx bundle

    Use when predicting conserved RNA-RNA interactions between two CLUSTAL alignments to identify evolutionary conserved binding sites, hybridization energies, and duplex structures.
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94. ▌
    Rnaconsensus · vimalinx bundle

    Use when predicting RNA secondary structures for single sequences using information from multiple sequence alignments of homologous sequences.
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95. ▌
    Rnamultifold · vimalinx bundle

    Use when predicting secondary structures and base pairing probabilities for multiple interacting RNA molecules
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96. ▌
    Starlong Avx · vimalinx bundle

    Use when aligning long RNA-seq reads to a reference genome with splice-aware mapping, or when generating STAR genome indices for long-read data.
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97. ▌
    Subtract Bed · vimalinx bundle

    Use when you need to remove overlapping portions of one interval set from another, such as subtracting blacklist, repeat, or annotation regions from BED, GFF, VCF, or BAM-like inputs.
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98. ▌
    Test Edirect · vimalinx bundle

    Use when smoke-testing an Entrez Direct installation with the bundled long-form example suite or the focused `-test` trace mode.
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99. ▌
    Vcf Annotate · vimalinx bundle

    Use when annotating VCF files with custom annotations, applying filters, or modifying INFO/ID/QUAL/FILTER columns.
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100. ▌
     Vcf Contrast · vimalinx bundle

     Use when comparing variant samples against background samples to identify unique genotypes and novel variants in VCF files.
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