esl-compalign

name	esl-compalign
description	Use when comparing a test multiple sequence alignment against a trusted reference alignment to compute accuracy. Requires Stockholm format files with
disable-model-invocation	true
user-invocable	true

esl-compalign

Quick Start

• Command: esl-compalign [-options] <trusted file> <test file>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-compalign
• Full reference: See references/help.md

When To Use This Tool

• Use esl-compalign when evaluating a test alignment against a trusted reference alignment.
• It is appropriate for benchmark or method-comparison workflows where both alignments are in Stockholm format with RF annotation.
• Use -c when you want per-column statistics and -p when comparing alignment accuracy against posterior probability information.
• Reach for it when you need an explicit quantitative comparison of alignment quality rather than just visual inspection.

Common Patterns

# Compare a test alignment against a trusted alignment
esl-compalign trusted.sto test.sto

# Emit per-column statistics instead of per-sequence statistics
esl-compalign -c trusted.sto test.sto

# Compare accuracy as a function of posterior probability
esl-compalign -p trusted.sto test.sto

# Write column-wise stats in ssdraw-compatible format
esl-compalign -c --c2dfile compalign.dfile trusted.sto test.sto

Recommended Workflow

1. Prepare trusted and test alignments in Stockholm format with #=GC RF markup
2. Verify sequences appear in identical order in both files
3. Confirm #=GC RF markup has identical number of non-gap characters in both files
4. Run esl-compalign <trusted file> <test file> to compute accuracy

Guardrails

• Both files must be in Stockholm format with #=GC RF markup
• Sequences must occur in the same order in the two files
• Number of non-gap characters in #=GC RF markup must be identical between files
• -p only makes sense when posterior probability annotation exists in the tested alignment context