esl-translate

name	esl-translate
description	Use when translating nucleotide sequences to amino acid sequences using Easel's translation utility from the HMMER suite.
disable-model-invocation	true
user-invocable	true

esl-translate

Quick Start

• Command: esl-translate [-options] <seqfile>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-translate
• Full reference: See references/help.md for detailed options (run esl-translate -h)

When To Use This Tool

• Use esl-translate when you need quick ORF-oriented translation of nucleotide sequences into amino acid sequences.
• It is appropriate for six-frame translation scans, ORF extraction, or testing alternative genetic codes before downstream protein-domain analysis.
• Use --watson or --crick when you only want one strand instead of both.
• Reach for -l, -m, or -M when you need to constrain the ORFs that are reported.

Common Patterns

# Default six-frame translation of nucleotide sequences
esl-translate transcripts.fa > orfs.fa

# Require longer ORFs
esl-translate -l 50 transcripts.fa > long_orfs.fa

# Restrict to Watson strand only
esl-translate --watson transcripts.fa > watson_orfs.fa

# Use bacterial genetic code and only AUG starts
esl-translate -c 11 -m transcripts.fa > bacterial_orfs.fa

Recommended Workflow

1. Prepare your nucleotide sequence file in a supported format
2. Run esl-translate -h to review available options
3. Execute esl-translate [-options] <seqfile> with desired options
4. Verify the translated output sequences are correct

Guardrails

• Use -h for help (not --help or --version which are unsupported)
• Input must be a valid sequence file <seqfile>
• Ensure input sequences are nucleotide (not already amino acid)
• -m and -M are stricter start-codon filters and can substantially reduce the number of reported ORFs