esl-afetch

name	esl-afetch
description	Use when retrieving specific multiple sequence alignments from an MSA file by name, or when indexing MSA files for faster access.
disable-model-invocation	true
user-invocable	true

esl-afetch

Tool from the HMMER suite for extracting named alignments from multiple sequence alignment files.

Quick Start

• Command: esl-afetch [options] <msafile> <name>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-afetch
• Full reference: See references/help.md for complete options and usage details

When To Use This Tool

• Use esl-afetch when you need to retrieve named alignments from a multi-alignment file.
• It is the alignment analogue of esl-sfetch: index once, then pull one or many alignments by key.
• Use -f for batch extraction and --outformat when the fetched alignments should be rewritten in another alignment format.
• It is useful when building alignment subsets or extracting specific families from large Stockholm/Pfam-style collections.

Common Patterns

# Index an MSA file
esl-afetch --index families.sto

# Fetch one named alignment
esl-afetch families.sto PF00001 > PF00001.sto

# Fetch many named alignments listed in a file
esl-afetch -f families.sto ids.txt > subset.sto

# Fetch and rewrite in aligned FASTA format
esl-afetch --outformat afa families.sto PF00001 > PF00001.afa

Recommended Workflow

1. Verify your MSA file format and identify target alignment names
2. Optionally index large MSA files with esl-afetch --index <msafile> for faster access
3. Retrieve alignments using either single name or batch mode with -f
4. Validate extracted alignments contain expected sequences

Guardrails

• Ensure alignment names match exactly as stored in the MSA file
• Use -f with a name file when retrieving multiple alignments efficiently
• Run esl-afetch -h for additional options (note: --help is not supported)
• --index creates an SSI sidecar and is the right first step for repeated lookups on large MSA collections