esl-alimap

name	esl-alimap
description	Use when comparing or mapping two multiple sequence alignments in Stockholm format to analyze their overlap or relationship.
disable-model-invocation	true
user-invocable	true

esl-alimap

Quick Start

• Command: esl-alimap [options] <msafile1> <msafile2>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-alimap
• Full reference: See references/help.md for detailed options (via esl-alimap -h)

When To Use This Tool

• Use esl-alimap when you need to map columns or RF positions between two related Stockholm alignments.
• It is useful for tracking how one alignment corresponds to another after trimming, masking, or subalignment extraction.
• Use it when you want 0/1 masks that project alignment columns or RF positions from one MSA onto another.
• Reach for --submap when the second alignment is known to be a strict subalignment of the first.

Common Patterns

# Print a column-by-column mapping between two Stockholm alignments
esl-alimap aln1.sto aln2.sto

# Suppress verbose per-column mapping and just emit summary information
esl-alimap -q aln1.sto aln2.sto

# Write a mask describing aln1 columns that map to aln2 RF positions
esl-alimap --mask-a2rf aln1_to_aln2.mask aln1.sto aln2.sto

# Generate a subalignment mask when aln2 is a subalignment of aln1
esl-alimap --submap sub.mask aln1.sto aln2.sto

Recommended Workflow

1. Prepare two MSAs in Stockholm format (required input format)
2. Run esl-alimap [options] <msafile1> <msafile2> with desired options
3. Review output to understand alignment mapping relationship
4. Use results to guide downstream comparative alignment analysis

Guardrails

• Both input files must be in Stockholm format
• Use -h for help (not --help or --version, which are unsupported)
• Ensure both alignments contain related sequences for meaningful mapping
• If alphabet guessing is ambiguous, force it with --amino, --dna, or --rna