vimalinx/bio-agent - Page 3

download-sequence

Use when downloading NCBI ASN.1 biological sequence archive divisions such as BCT, PLN, or VRL into the current directory.

ds2pme

Use when converting PubMed `DocumentSummary` XML into `Pubmed-entry` ASN.1 text, or into the intermediate XML form before final ASN.1 flattening.

dustmasker

Use when masking low-complexity regions in nucleotide sequences using the Symmetric DUST algorithm before BLAST searches or other sequence analyses.

easel

Use when invoking the top-level `easel` dispatcher to discover or run Easel sequence-analysis subcommands from the HMMER toolchain.

ecollect

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

ecommon-sh

Use when auditing or reusing the shared EDirect shell functions that other Entrez Direct wrapper scripts source internally.

efetch

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

efilter

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

einfo

Use when you need to discover available NCBI Entrez databases, explore searchable fields within a specific database, or identify cross-database links for building EDirect queries.

elink

Use when you need to navigate relationships between records in NCBI Entrez databases, find related articles, track citations, or link records across different databases such as PubMed to Protein.

epost

Use when you need to post unique identifiers or accession numbers to NCBI Entrez databases for subsequent retrieval operations

esample

Use when printing canned sample NCBI XML, JSON, flatfile, or GFF documents for testing, parser development, or xtract query prototyping.

esearch

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.

esl-afetch

Use when retrieving specific multiple sequence alignments from an MSA file by name, or when indexing MSA files for faster access.

esl-alimanip

Use when manipulating multiple sequence alignment files using Easel tools from HMMER.

esl-alimap

Use when comparing or mapping two multiple sequence alignments in Stockholm format to analyze their overlap or relationship.

esl-alimask

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.

esl-alimerge

Use when merging multiple sequence alignment files in Stockholm or Pfam format into a single alignment.

esl-alipid

Use when calculating pairwise percent identities from multiple sequence alignments in FASTA or Stockholm format.

esl-alirev

Use when you need to reverse sequences in a multiple sequence alignment file. Part of the Easel toolkit distributed with HMMER.

esl-alistat

Use when working with alignment files and needing statistics from HMMER's Easel toolkit.

esl-compalign

Use when comparing a test multiple sequence alignment against a trusted reference alignment to compute accuracy. Requires Stockholm format files with

esl-compstruct

Use when comparing two Stockholm format files with secondary structure markup to evaluate how well a test structure matches a trusted reference.

esl-construct

Use when inspecting, comparing, or rebuilding consensus RNA/DNA secondary-structure annotation in Stockholm alignments.

esl-histplot

Use when turning one numeric value per line into Easel or xmgrace histogram or survival-plot data for score-distribution analysis.

esl-mask

Use when applying coordinate-based masks to named sequences in FASTA or other Easel-supported sequence files.

esl-mixdchlet

Use when fitting, scoring, generating, or sampling mixture Dirichlet priors for count-vector data used in HMMER or Infernal-style models.

esl-reformat

Use when you need to convert sequence files between different formats such as FASTA, Stockholm, A2M, Clustal, or Phylip.

esl-selectn

Use when reservoir-sampling a fixed number of random lines from a large text file or stream without loading the whole file.

esl-seqrange

Use when splitting an SSI-indexed sequence file into per-process sequence-index ranges for embarrassingly parallel Easel or HMMER jobs.

esl-seqstat

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.

esl-sfetch

Use when you need to extract specific sequences by name from a sequence file, or index a sequence file for faster lookup.

esl-shuffle

Use when shuffling biological sequences, bootstrapping alignment columns, or generating de novo random RNA, DNA, or protein controls.

esl-ssdraw

Use when converting a Stockholm RNA or DNA alignment plus a PostScript structure template into colored secondary-structure diagrams.

esl-translate

Use when translating nucleotide sequences to amino acid sequences using Easel's translation utility from the HMMER suite.

esl-weight

Use when adding Stockholm sequence-weight annotations to nucleotide or protein MSAs before downstream HMMER-style modeling.

esummary

Use when fetching document summaries from NCBI Entrez databases by database name and identifier or accession

evo2

Use when working from the local Evo 2 repository for DNA-sequence scoring, embeddings, generation, or phage-genome design experiments.

exact-snp

Use when calling SNPs from aligned SAM/BAM reads with Subread's `exactSNP` variant caller.

exclude-uid-lists

Use when subtracting one Entrez or NCBI UID file from another and keeping only IDs unique to the first file.