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