All Skills

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.

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.

Use when working with FASTA or FASTQ files for statistics, filtering, transformation, format conversion, searching, or set operations.

Use when converting ACE assembly files into SAM while preserving legacy ACE-specific padded or contig-sequence behavior.

Use when masking columns or coordinate ranges in multiple-sequence alignments before downstream HMMER or alignment-processing steps.

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

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.

Use when converting CSV-style tabular data into XML for downstream EDirect or XML-based processing.

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

Use when filling ancestral alleles into the INFO column of VCF files using ancestral alignment data from 1000 Genomes or similar sources.

Use when annotating VCF files with flanking sequence information (INFO/FS tag) or masking regions/variants in flanking sequences.

Use when converting FASTA sequence records into XML for downstream EDirect or XML-based sequence processing.

Use when converting GenBank format files to table format as part of the Entrez Direct toolkit from bioconda.

Use when converting GenBank flatfiles into XML for downstream EDirect or XML-based sequence annotation workflows.

Use when a GFF file needs bcftools/csq-compatible gene and transcript attributes before consequence annotation.

Use when sampling synthetic sequences, alignments, or consensus sequences from one or more profile HMMs.

Use when extracting per-position residue-height and indel-rate data from a profile HMM for sequence-logo visualization.

Use when running HMMER master or worker daemon services that front `phmmer`, `hmmsearch`, and `hmmscan` against cached databases.

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.

Use when converting INI-style configuration files into XML for downstream EDirect or XML-based processing.

Use when inferring maximum-likelihood phylogenetic trees, selecting substitution models, running bootstrap support analyses, or performing partitioned phylogenetic analyses on sequence alignments.

Use when you need to aggregate quality control reports from multiple bioinformatics tools into a single HTML report

Use when profiling nucleotide content (AT/GC percentages, base counts) of genomic intervals against a FASTA reference.

Use when converting `PubmedArticle` XML from EDirect into APA-style citation text or APA-structured XML for downstream parsing.

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

Use when computing RNA specific heat profiles from sequence data to analyze melting behavior and thermal stability across temperature ranges.

Use when performing pairwise structural alignments of RNA sequences that incorporate both sequence and structure information through base pair propensity vectors.

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

Use when converting SCN-format records into XML for downstream EDirect or XML-based processing.

Use when converting NCBI dbSNP docsum XML into flat tabular rows through the bundled `snp2hgvs | hgvs2spdi | spdi2tbl` pipeline.

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.

Use when converting tabular text into XML for downstream EDirect or XML-based processing.

Use when searching protein query sequences against a translated nucleotide database to identify protein-coding regions or homologs in genomic data.

Use when converting NCBI XML sequence records to FASTA format, typically after fetching data with efetch from the Entrez Direct toolkit.

Use when extracting INSDSeq XML feature tables into tab-delimited text for downstream parsing or annotation review.

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