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vimalinx

@vimalinx source repo

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1. ▌
   Rnapkplex · vimalinx bundle

   Use when searching an RNA sequence for pseudoknot-forming interactions by combining local accessibility with interaction energy, especially when ordinary pseudoknot-free folding is insufficient.
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2. ▌
   Rnaplfold · vimalinx bundle

   Use when computing local RNA secondary structure pair probabilities, scanning large genomes for short stable RNA structures, or analyzing unpaired region probabilities across sliding windows.
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3. ▌
   Rnasubopt · vimalinx bundle

   Use when computing suboptimal RNA secondary structures within an energy range above the minimum free energy, or when sampling structures from the Boltzmann ensemble.
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4. ▌
   Segmasker · vimalinx bundle

   Use when identifying and masking low-complexity regions in protein sequences with the SEG algorithm before BLAST or other downstream analyses.
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5. ▌
   Shift Bed · vimalinx bundle

   Use when you need to shift genomic intervals in BED/GFF/VCF files by a specified number of base pairs, either uniformly or strand-specifically.
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6. ▌
   Star Avx2 · vimalinx bundle

   Use when aligning RNA-seq reads to a reference genome or generating genome indices for spliced transcript alignment
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7. ▌
   Star Sse3 · vimalinx bundle

   Use when aligning RNA-seq reads to a reference genome with splice-aware mapping, generating genome indexes, or performing splice junction detection.
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8. ▌
   Test Pcre · vimalinx bundle

   Use when testing or benchmarking PCRE2 regular expressions with the local `test_pcre` / `pcre2test` executable.
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9. ▌
   Transmute · vimalinx bundle

   Use when invoking the public `transmute` wrapper for format conversion, sequence editing, or shell-level helper modes that may be intercepted before dispatch to the platform binary.
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10. ▌
    Vcf Merge · vimalinx bundle

    Use when merging multiple VCF files by genomic position to create multi-sample VCFs from individual or fewer-sample VCFs.
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11. ▌
    Vcf Query · vimalinx bundle

    Use when extracting and formatting specific fields from compressed VCF files, querying variants by region, or generating custom tabular output with genotype and INFO data.
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12. ▌
    Vcf Stats · vimalinx bundle

    Use when computing statistics on VCF files, filtering variant data by quality or fields, or generating summary reports from gzipped VCF inputs.
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13. ▌
    Args2slice · vimalinx bundle

    Use when inspecting shell argument tokenization by printing argv as a Go-style `[]string` literal.
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14. ▌
    Bam To Bed · vimalinx bundle

    Use when converting BAM alignment files to BED6, BED12, or BEDPE format for downstream analysis or visualization.
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15. ▌
    Bed To Bam · vimalinx bundle

    Use when converting BED/GFF/VCF feature records to BAM format for visualization or downstream analysis.
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16. ▌
    Bed To Igv · vimalinx bundle

    Use when you need to generate an IGV batch script for taking snapshots at loci defined in BED, GFF, or VCF files, especially for repeatable visual review of many regions.
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17. ▌
    Blastdbcmd · vimalinx bundle

    Use when retrieving sequences or metadata from local BLAST databases, looking up entries by identifier or taxonomy, or inspecting database contents.
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18. ▌
    Blastn · vimalinx bundle

    Use when performing nucleotide-nucleotide similarity searches to identify homologs, annotate sequences, or compare query sequences against nucleotide databases.
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19. ▌
    Blastp · vimalinx bundle

    Use when comparing protein sequences against protein databases for similarity searches, homology detection, or functional annotation.
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20. ▌
    Blastx · vimalinx bundle

    Use when comparing translated nucleotide query sequences against protein databases to identify homologous proteins and potential protein-coding regions.
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21. ▌
    Ds2pme · vimalinx bundle

    Use when converting PubMed `DocumentSummary` XML into `Pubmed-entry` ASN.1 text, or into the intermediate XML form before final ASN.1 flattening.
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22. ▌
    Efetch · vimalinx bundle

    Use when you need to fetch records or data from NCBI Entrez databases (PubMed, nucleotide, protein, gene, SRA, etc.) by ID or accession
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23. ▌
    Fastqc · vimalinx bundle

    Use when you need to perform quality control analysis on high-throughput sequencing data (fastq, bam, sam, or fast5 files) to identify potential problems before downstream analysis.
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24. ▌
    Hisat2 · vimalinx bundle

    Use when aligning RNA-seq reads to a reference genome using graph-based indexing for fast and sensitive spliced alignment.
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25. ▌
    Hmmsim · vimalinx bundle

    Use when you need to characterize score distributions of a profile HMM on random sequences, such as calibration checks, benchmarking, or filter-behavior experiments.
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26. ▌
    Iqtree · vimalinx bundle

    Use when inferring maximum-likelihood phylogenies from aligned sequences, performing automated model selection, or assessing branch support with bootstrap or aLRT methods
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27. ▌
    Muscle · vimalinx bundle

    Use when performing multiple sequence alignment of FASTA inputs, generating alignment ensembles, or calculating alignment confidence metrics.
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28. ▌
    Nhmmer · vimalinx bundle

    Use when searching DNA or RNA queries against nucleotide sequence databases with HMMER's nucleotide homology search engine.
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29. ▌
    Nquire · vimalinx bundle

    Use when making raw HTTP, E-utilities, PubChem, datasets, or FTP requests through the low-level EDirect transport wrapper.
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30. ▌
    Phmmer · vimalinx bundle

    Use when searching one or more protein query sequences against a protein sequence database with HMMER's one-pass sequence-vs-sequence searcher.
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31. ▌
    Rchive · vimalinx bundle

    Use when building, indexing, or querying local XML record archives from NCBI Entrez databases, creating inverted indices, or managing PubMed local caches.
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32. ▌
    Repair · vimalinx bundle

    Use when paired-end reads need to be reordered so mates appear consecutively, or when preparing BAM files for featureCounts by adding dummy reads for singletons.
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33. ▌
    Rnados · vimalinx bundle

    Use when summarizing an RNA folding landscape by counting how many structures fall into each energy band, rather than enumerating individual folds one by one.
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34. ▌
    Seqkit · vimalinx bundle

    Use when working with FASTA or FASTQ files for statistics, filtering, transformation, format conversion, searching, or set operations.
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35. ▌
    Xfetch · vimalinx bundle

    Use when retrieving records from a local EDirect archive via the `x*` local-cache stack, not when calling the remote NCBI `efetch` service directly.
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36. ▌
    Xtract · vimalinx bundle

    Use when parsing, extracting, or converting XML data from NCBI Entrez or other bioinformatics sources into tab-delimited tables. Use for selecting specific elements, filtering records, and restructuring hierarchical XML into flat formats for downstream analysis.
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37. ▌
    Ace2sam · vimalinx bundle

    Use when converting ACE assembly files into SAM while preserving legacy ACE-specific padded or contig-sequence behavior.
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38. ▌
    Alimask · vimalinx bundle

    Use when masking columns or coordinate ranges in multiple-sequence alignments before downstream HMMER or alignment-processing steps.
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39. ▌
    Asn2ref · vimalinx bundle

    Use when converting `Seq-entry` ASN.1/XML-like citation content into compact `CITATION` XML blocks for EDirect-style matching workflows.
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40. ▌
    Asn2xml · vimalinx bundle

    Use when converting NCBI-style ASN.1 payloads into XML for downstream EDirect or XML-based processing.
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41. ▌
    Blst2gm · vimalinx bundle

    Use when converting compatible BLAST annotation XML/ASN streams into a compact gene-markup-style table for downstream EDirect interval helpers.
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42. ▌
    Bowtie2 · vimalinx bundle

    Use when aligning short reads to a reference genome or indexed sequence database. Suitable for mapping FASTQ/FASTA reads in paired-end or single-end mode to produce SAM output.
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43. ▌
    Csv2xml · vimalinx bundle

    Use when converting CSV-style tabular data into XML for downstream EDirect or XML-based processing.
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44. ▌
    Efilter · vimalinx bundle

    Use when filtering Entrez search results by date, organism, publication type, sequence features, or other database-specific criteria in bioinformatics pipelines.
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45. ▌
    Esample · vimalinx bundle

    Use when printing canned sample NCBI XML, JSON, flatfile, or GFF documents for testing, parser development, or xtract query prototyping.
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46. ▌
    Esearch · vimalinx bundle

    Use when searching NCBI Entrez databases (pubmed, gene, protein, nuccore, snp, geoprofiles) with query strings and field qualifiers to retrieve record UIDs for downstream processing.
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47. ▌
    Fill Aa · vimalinx bundle

    Use when filling ancestral alleles into the INFO column of VCF files using ancestral alignment data from 1000 Genomes or similar sources.
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48. ▌
    Fill Fs · vimalinx bundle

    Use when annotating VCF files with flanking sequence information (INFO/FS tag) or masking regions/variants in flanking sequences.
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49. ▌
    Fsa2xml · vimalinx bundle

    Use when converting FASTA sequence records into XML for downstream EDirect or XML-based sequence processing.
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50. ▌
    Gbf2fsa · vimalinx bundle

    Use when converting GenBank format (.gbf) files to FASTA format (.fsa) as part of sequence data preprocessing
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51. ▌
    Gbf2ref · vimalinx bundle

    Use when working with GenBank format files and need to create reference indexers for sequence data retrieval or processing within the Entrez Direct toolkit.
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52. ▌
    Gbf2tbl · vimalinx bundle

    Use when converting GenBank format files to table format as part of the Entrez Direct toolkit from bioconda.
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53. ▌
    Gbf2xml · vimalinx bundle

    Use when converting GenBank flatfiles into XML for downstream EDirect or XML-based sequence annotation workflows.
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54. ▌
    Gff2gff · vimalinx bundle

    Use when a GFF file needs bcftools/csq-compatible gene and transcript attributes before consequence annotation.
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55. ▌
    Gff2xml · vimalinx bundle

    Use when converting GFF or GFF3 feature annotations into structured XML for downstream EDirect-style processing.
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56. ▌
    Gm2segs · vimalinx bundle

    Use when converting BLASTN mRNA alignment XML into segmented interval reports and strand-overlap summaries in EDirect pipelines.
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57. ▌
    Hmmemit · vimalinx bundle

    Use when sampling synthetic sequences, alignments, or consensus sequences from one or more profile HMMs.
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58. ▌
    Hmmlogo · vimalinx bundle

    Use when extracting per-position residue-height and indel-rate data from a profile HMM for sequence-logo visualization.
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59. ▌
    Hmmpgmd · vimalinx bundle

    Use when running HMMER master or worker daemon services that front `phmmer`, `hmmsearch`, and `hmmscan` against cached databases.
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60. ▌
    Hmmscan · vimalinx bundle

    Use when searching protein sequences against profile hidden Markov models (HMMs) such as Pfam or other HMM databases.
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61. ▌
    Hmmstat · vimalinx bundle

    Use when you need to inspect and summarize statistics for HMM (profile hidden Markov model) files from the HMMER suite.
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62. ▌
    Htsfile · vimalinx bundle

    Use when you need to identify, view, or copy HTS-format files (BAM, CRAM, VCF, BCF). Use for inspecting file headers or viewing textual representations of binary HTS files.
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63. ▌
    Ini2xml · vimalinx bundle

    Use when converting INI-style configuration files into XML for downstream EDirect or XML-based processing.
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64. ▌
    Iqtree3 · vimalinx bundle

    Use when inferring maximum-likelihood phylogenetic trees, selecting substitution models, running bootstrap support analyses, or performing partitioned phylogenetic analyses on sequence alignments.
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65. ▌
    Kinfold · vimalinx bundle

    Use when simulating stochastic folding kinetics of single-stranded nucleic acids, computing first passage times between structures, or analyzing RNA/DNA folding trajectories.
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66. ▌
    Map Bed · vimalinx bundle

    Use when you need to apply aggregation functions (sum, mean, count, etc.) to values from overlapping intervals in one file and map them onto intervals from another file.
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67. ▌
    Multiqc · vimalinx bundle

    Use when you need to aggregate quality control reports from multiple bioinformatics tools into a single HTML report
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68. ▌
    Nuc Bed · vimalinx bundle

    Use when profiling nucleotide content (AT/GC percentages, base counts) of genomic intervals against a FASTA reference.
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69. ▌
    Pma2apa · vimalinx bundle

    Use when converting `PubmedArticle` XML from EDirect into APA-style citation text or APA-structured XML for downstream parsing.
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70. ▌
    Pma2pme · vimalinx bundle

    Use when converting `PubmedArticle` XML into `Pubmed-entry` ASN.1 text, or into the intermediate XML form used before final ASN.1 emission.
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71. ▌
    Rnaeval · vimalinx bundle

    Use when evaluating the free energy (kcal/mol) of an RNA secondary structure, calculating co-folding energies for two RNA strands, or analyzing consensus structures from multiple sequence alignments.
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72. ▌
    Rnafold · vimalinx bundle

    Use when predicting RNA secondary structures, calculating minimum free energy (MFE) folds, or computing partition functions and base pairing probabilities for RNA sequences.
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73. ▌
    Rnaheat · vimalinx bundle

    Use when computing RNA specific heat profiles from sequence data to analyze melting behavior and thermal stability across temperature ranges.
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74. ▌
    Rnapaln · vimalinx bundle

    Use when performing pairwise structural alignments of RNA sequences that incorporate both sequence and structure information through base pair propensity vectors.
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75. ▌
    Rnaplex · vimalinx bundle

    Use when screening a small query RNA against longer target RNA sequences for inter-molecular hybridization sites, especially when optional RNAplfold accessibility profiles should influence the ranking.
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76. ▌
    Rnaplot · vimalinx bundle

    Use when visualizing RNA secondary structures from dot-bracket notation or Stockholm alignments, generating structure diagrams, or creating annotated consensus structure plots.
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77. ▌
    Roh Viz · vimalinx bundle

    Use when turning `bcftools roh` output plus a VCF/BCF into an interactive HTML visualization of ROH segments and homozygosity rates.
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78. ▌
    Scn2xml · vimalinx bundle

    Use when converting SCN-format records into XML for downstream EDirect or XML-based processing.
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79. ▌
    Snp2tbl · vimalinx bundle

    Use when converting NCBI dbSNP docsum XML into flat tabular rows through the bundled `snp2hgvs | hgvs2spdi | spdi2tbl` pipeline.
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80. ▌
    Subjunc · vimalinx bundle

    Use when aligning RNA-seq reads to a reference genome with junction detection, including exon-exon junctions and gene fusions.
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81. ▌
    Sublong · vimalinx bundle

    Use when aligning long FASTQ reads to a reference genome with Subread's long-read aligner, optionally in RNA-seq mode.
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82. ▌
    Tag Bam · vimalinx bundle

    Use when you need to annotate BAM alignments with a two-character tag based on overlaps with BED, GFF, or VCF annotation files, such as labeling reads by feature class or interval source.
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83. ▌
    Tbl2xml · vimalinx bundle

    Use when converting tabular text into XML for downstream EDirect or XML-based processing.
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84. ▌
    Tblastn · vimalinx bundle

    Use when searching protein query sequences against a translated nucleotide database to identify protein-coding regions or homologs in genomic data.
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85. ▌
    Tblastx · vimalinx bundle

    Use when searching nucleotide sequences against a nucleotide database using translated protein comparison. Useful for detecting distant evolutionary relationships between nucleotide sequences.
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86. ▌
    Xfilter · vimalinx bundle

    Use when filtering a UID stream against a local postings index with a query expression in the `x*` local-archive toolchain.
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87. ▌
    Xml2fsa · vimalinx bundle

    Use when converting NCBI XML sequence records to FASTA format, typically after fetching data with efetch from the Entrez Direct toolkit.
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88. ▌
    Xml2tbl · vimalinx bundle

    Use when extracting INSDSeq XML feature tables into tab-delimited text for downstream parsing or annotation review.
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89. ▌
    Xsearch · vimalinx bundle

    Use when searching a local NCBI EDirect archive/postings index with Boolean, title, word, or pair queries inside the `x*` local-cache workflow.
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90. ▌
    Bcftools · vimalinx bundle

    Use when working with VCF/BCF variant files for indexing, manipulation, analysis, or variant calling.
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91. ▌
    Bedtools · vimalinx bundle

    Use when performing genome arithmetic on interval files (BED, BAM, BEDGRAPH), including intersection, merging, coverage, format conversion, or sequence extraction.
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92. ▌
    Cit2pmid · vimalinx bundle

    Use when resolving structured citation fields or citation XML into candidate PubMed IDs with EDirect matching modes.
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93. ▌
    Clustalw · vimalinx bundle

    Use when performing multiple sequence alignments on protein or nucleotide sequences, generating phylogenetic trees, or producing alignment output in various formats.
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94. ▌
    Cutadapt · vimalinx bundle

    Use when you need to remove adapter sequences from high-throughput sequencing reads, trim low-quality bases, or filter reads by length. Supports single-end and paired-end FASTQ/FASTA input with error-tolerant adapter matching.
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95. ▌
    Datatool · vimalinx bundle

    Use when working with NCBI ASN.1 module files, schema exports, or ASN.1/XML conversion tasks that require the `datatool` command.
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96. ▌
    Ecollect · vimalinx bundle

    Use when collecting sorted UID lists from EDirect query sources such as PubMed queries, explicit IDs, WebEnv history state, or input files.
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97. ▌
    Bwa · vimalinx bundle

    Use when aligning low-divergence DNA sequence reads to a reference genome
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98. ▌
    B2ct · vimalinx bundle

    Use when converting ViennaRNA-style sequence-plus-dot-bracket records on stdin into RNA connectivity-table output.
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99. ▌
    Evo2 · vimalinx

    Use when working from the local Evo 2 repository for DNA-sequence scoring, embeddings, generation, or phage-genome design experiments.
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100. ▌
     Popt · vimalinx bundle

     Use when filtering `RNAsubopt -s` output to keep p-optimal RNA structures in a ViennaRNA post-processing pipeline.
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