esl-alistat

name	esl-alistat
description	Use when working with alignment files and needing statistics from HMMER's Easel toolkit.
disable-model-invocation	true
user-invocable	true

esl-alistat

Quick Start

• Command: esl-alistat [options] <alignment_file>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-alistat
• Reference: See references/help.md for detailed options

When To Use This Tool

• Use esl-alistat when you need summary statistics on one or more multiple sequence alignments rather than on raw sequences.
• It is suited to alignment-level questions such as average identity, alignment length, composition, and annotation-derived information content summaries.
• Use it before HMM construction, masking, or curation when you want to inspect alignment quality and content.
• In this environment it is currently blocked by a shared-library issue, so treat it as documented-but-not-runnable until the dependency is repaired.

Common Patterns

# Basic alignment statistics
esl-alistat alignment.sto

# Write a per-alignment list report
esl-alistat --list alns.list alignment.sto

# Export information-content and composition reports
esl-alistat --icinfo ic.txt --cinfo comp.txt alignment.sto

# Export pairwise-identity or posterior-probability related reports when present
esl-alistat --pcinfo pc.txt --psinfo ps.txt alignment.sto

Recommended Workflow

1. Verify shared library dependencies are satisfied before use.
2. Start with a plain esl-alistat <alignment_file> run to confirm the binary works in the current environment.
3. Add report-output options such as --list, --icinfo, --cinfo, or --bpinfo only if the input alignment carries the needed annotation.
4. Review the generated reports before downstream masking, trimming, or HMM building.

Guardrails

• Current installation missing libopenblas.so.0; may require environment repair
• Help text unavailable due to library loading error; rely on references/help.md
• Confirm HMMER package is fully installed and functional before use
• Options such as --pcinfo, --psinfo, --iinfo, and --bpinfo depend on specific alignment annotations and will fail if those annotations are absent