esl-alirev

name	esl-alirev
description	Use when you need to reverse sequences in a multiple sequence alignment file. Part of the Easel toolkit distributed with HMMER.
disable-model-invocation	true
user-invocable	true

esl-alirev

Quick Start

• Command: esl-alirev [-options] <msafile>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-alirev
• Full reference: See references/help.md for detailed options (use esl-alirev -h to view)

When To Use This Tool

• Use esl-alirev when an alignment must be reverse-complemented as an alignment rather than as individual raw sequences.
• It is appropriate for DNA or RNA MSAs where the reverse orientation is needed for comparison or downstream analysis.
• Use it when you need the output alignment preserved in a chosen MSA format via --outformat.
• This is not a generic nucleotide reverse-complement tool for unaligned FASTA; it is alignment-oriented.

Common Patterns

# Reverse-complement an RNA alignment
esl-alirev --rna alignment.sto > alignment.rev.sto

# Reverse-complement a DNA alignment and emit aligned FASTA
esl-alirev --dna --outformat afa alignment.sto > alignment.rev.afa

# Declare the input format explicitly
esl-alirev --informat stockholm --rna alignment.sto > alignment.rev.sto

Recommended Workflow

1. Verify your input MSA file format is supported by Easel
2. Run esl-alirev -h to review available options
3. Execute esl-alirev [options] <msafile> on your alignment
4. Validate the output alignment contains reversed sequences as expected

Guardrails

• Use -h (not --help or --version) to access help
• Ensure input file is a valid multiple sequence alignment
• Check output integrity after reversal operations
• Set --dna or --rna explicitly so the reverse-complement logic uses the correct alphabet