esl-seqstat

name	esl-seqstat
description	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.
disable-model-invocation	true
user-invocable	true

esl-seqstat

Quick Start

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

When To Use This Tool

• Use esl-seqstat when you need a quick summary of a sequence file before downstream modeling, search, or translation.
• It is appropriate for counting records, checking length ranges, and optionally reporting residue composition.
• Use -a when you want per-sequence lines instead of just one summary block.
• Reach for --dna, --rna, or --amino when automatic alphabet detection is ambiguous.

Common Patterns

# Basic summary statistics for a sequence file
esl-seqstat sequences.fa

# Report per-sequence information
esl-seqstat -a sequences.fa

# Include residue composition in the report
esl-seqstat -c sequences.fa

# Force RNA alphabet interpretation
esl-seqstat --rna transcripts.fa

Recommended Workflow

1. Verify your sequence file format is supported by Easel/HMMER tools
2. Run esl-seqstat <seqfile> to obtain basic statistics
3. Review output for expected sequence count and length ranges
4. Proceed with downstream HMMER analyses if statistics look correct

Guardrails

• Use esl-seqstat -h for help; --help and --version are not supported flags
• Ensure the input sequence file exists and is readable before running
• This tool only reports statistics; it does not modify or filter sequences
• --comptbl changes the output style to a composition table rather than the default human-readable summary