esl-reformat

name	esl-reformat
description	Use when you need to convert sequence files between different formats such as FASTA, Stockholm, A2M, Clustal, or Phylip.
disable-model-invocation	true
user-invocable	true

esl-reformat

Quick Start

• Command: esl-reformat [-options] <format> <seqfile>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-reformat
• Full reference: See references/help.md for complete format options

When To Use This Tool

• Use esl-reformat when you need to convert sequence or alignment files between Easel-supported formats.
• It is appropriate for both unaligned sequence files and aligned MSA formats such as Stockholm, AFA, Clustal, and Phylip.
• Use it when downstream HMMER/Easel tools require a specific format or when you want to normalize case, alphabet, gaps, or naming during conversion.
• It is also handy for simple alignment cleanup such as dropping all-gap columns with --mingap or all gapped columns with --nogap.

Common Patterns

# Convert Stockholm alignment to aligned FASTA
esl-reformat afa alignment.sto > alignment.afa

# Convert FASTA DNA to RNA alphabet
esl-reformat -r fasta transcripts.fa > transcripts.rna.fa

# Remove all-gap columns from an alignment during conversion
esl-reformat --mingap stockholm alignment.sto > alignment.trimmed.sto

# Rename sequences sequentially in the output
esl-reformat --rename seq fasta sequences.fa > renamed.fa

Recommended Workflow

1. Identify your input sequence file and desired output format
2. Check available options: esl-reformat -h
3. Run conversion: esl-reformat <format> <seqfile> > output.ext
4. Verify output format and sequence integrity

Guardrails

• Use -h for help; --help and --version are not valid options
• Output format must match one of the supported formats exactly
• Input file must contain recognizable sequence data in a supported format
• Some options only make sense for alignments (--mingap, --nogap) or for specific output formats (for example --namelen with PHYLIP)