esl-weight

name	esl-weight
description	Use when adding Stockholm sequence-weight annotations to nucleotide or protein MSAs before downstream HMMER-style modeling.
disable-model-invocation	true
user-invocable	true

esl-weight

Quick Start

• Command: esl-weight [options] <msafile>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-weight
• Full reference: See references/help.md for the current startup failure; option details below are grounded in the local man page plus binary strings.

When To Use This Tool

• Use esl-weight when you need per-sequence weights written back into a multiple alignment as Stockholm #=GS <seqname> WT <weight> annotation.
• It is useful before downstream profile-model building or when you want an explicit, inspectable weighted alignment artifact.
• Reach for -g for Gerstein/Sonnhammer/Chothia weights, -p for Henikoff position-based weights, or -b for BLOSUM-style cluster weights.

Common Patterns

# Default Gerstein/Sonnhammer/Chothia weighting
esl-weight alignment.sto > weighted.sto

# Faster Henikoff position-based weighting
esl-weight -p alignment.sto > pb-weighted.sto

# BLOSUM-style clustering weights at a chosen identity threshold
esl-weight -b --id 0.70 alignment.sto > blosum70.sto

# Force protein alphabet when autodetection is ambiguous
esl-weight --amino alignment.sto > weighted-aa.sto

Recommended Workflow

1. Fix the local shared-library issue first so the binary can start.
2. Prepare the input multiple alignment and force the alphabet with --amino, --dna, or --rna if autodetection could be ambiguous.
3. Choose the weighting rule that matches the downstream method.
4. Inspect the emitted Stockholm alignment and confirm #=GS ... WT lines are present.
5. Feed the weighted alignment into the next modeling step only after the annotations look plausible.

Guardrails

• The local executable currently fails to start because libopenblas.so.0 is missing. Until that library issue is fixed, -h and live runtime validation are unavailable.
• Despite the startup failure, the local man page documents -g as the default, -p as Henikoff position-based weighting, and -b as BLOSUM-style clustering weights.
• --id <x> only applies with -b; the documented default threshold is 0.62.
• Output is written in Stockholm format with WT annotations even if the input alignment came from another accepted format.
• Option details here are intentionally conservative because the current environment cannot execute the binary end-to-end.