esl-alimerge

name	esl-alimerge
description	Use when merging multiple sequence alignment files in Stockholm or Pfam format into a single alignment.
disable-model-invocation	true
user-invocable	true

esl-alimerge

Quick Start

• Command: esl-alimerge [options] <alignment file 1> <alignment file 2>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-alimerge
• Full reference: See references/help.md for complete options

When To Use This Tool

• Use esl-alimerge when you need to merge two or more related alignments using their RF annotation as the coordinate system.
• It is appropriate for Stockholm or Pfam alignments that represent compatible views of the same family or consensus space.
• Use --list when the merge spans more than two input alignment files.
• Reach for --rfonly when only RF-supported columns should survive in the merged result.

Common Patterns

# Merge two Stockholm/Pfam alignments
esl-alimerge aln1.sto aln2.sto > merged.sto

# Merge many alignments listed in a file
esl-alimerge --list merge.list > merged.sto

# Write merged output in aligned FASTA format
esl-alimerge --outformat afa aln1.sto aln2.sto > merged.afa

# Keep only RF-supported columns in the merged alignment
esl-alimerge --rfonly aln1.sto aln2.sto > merged_rfonly.sto

Recommended Workflow

1. Verify all input alignment files are in Stockholm or Pfam format
2. For two files, run esl-alimerge [options] file1.sto file2.sto
3. For more than two files, create a list file and run esl-alimerge --list <listfile>
4. Specify output format with relevant options if needed (stockholm is default)

Guardrails

• Input files must be Stockholm or Pfam format only
• Use -h for additional help options; --version and --help are not supported
• Ensure all alignments being merged share compatible sequence naming conventions
• -v only makes sense together with -o, because the merge report goes to stdout otherwise