esl-construct

name	esl-construct
description	Use when inspecting, comparing, or rebuilding consensus RNA/DNA secondary-structure annotation in Stockholm alignments.
disable-model-invocation	true
user-invocable	true

esl-construct

Quick Start

• Command: esl-construct [options] <msafile>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-construct
• Full reference: See references/help.md for --help failure behavior and esl-construct -h output

When To Use This Tool

• Use esl-construct when a Stockholm RNA/DNA alignment already contains individual structure annotation (#=GR SS), consensus structure annotation (#=GC SS_cons), or both, and you need to inspect how they agree or conflict.
• Use it to summarize which sequences carry structures and how many basepairs overlap with or conflict against SS_cons.
• Reach for structure-definition modes when you need to derive a replacement consensus structure from individual annotations: -x, -r, -c, --indi, --ffreq, or --fmin.
• Use -l and --lmax when you want a separate list of sequences that conflict with the current consensus structure.

Common Patterns

# Summarize existing structure annotation and conflicts
esl-construct alignment.sto

# Verbosely list conflicting individual basepairs
esl-construct -v alignment.sto

# Build a maximal non-conflicting consensus structure
esl-construct -x -o consensus.sto alignment.sto

# Use one named sequence's structure as the new consensus and RF annotation
esl-construct --indi seq42 --rfindi -o from-seq.sto alignment.sto

# Remove consensus basepairs that conflict with any individual structure
esl-construct -r -o pruned.sto alignment.sto

Recommended Workflow

1. Confirm the input alignment is Stockholm format, contains RNA or DNA sequences, and carries WUSS-compatible structure annotation.
2. Run the default mode or add -v to inspect how individual structures compare to any existing SS_cons.
3. Choose a consensus-definition strategy only after checking the conflict profile.
4. When rebuilding SS_cons, add -o <file> and optionally --pfam if you want non-interleaved Pfam-style Stockholm output.
5. Review the new SS_cons and any updated RF annotation before using the alignment downstream.

Guardrails

• Input must be Stockholm format and contain RNA or DNA, not protein sequences.
• -h works; --help and --version are rejected by the local executable.
• Any of -x, -r, -c, --indi, --ffreq, or --fmin requires -o.
• --rfc only applies with -c, and --rfindi only applies with --indi.
• Vienna dot-parentheses are accepted, but the tool interprets structure annotation in WUSS terms; malformed structure tags will break the workflow.