Use when comparing or mapping two multiple sequence alignments in Stockholm format to analyze their overlap or relationship.
esl-alimap [options] <msafile1> <msafile2>/home/vimalinx/miniforge3/envs/bio/bin/esl-alimapreferences/help.md for detailed options (via esl-alimap -h)esl-alimap when you need to map columns or RF positions between two related Stockholm alignments.--submap when the second alignment is known to be a strict subalignment of the first.# 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
esl-alimap [options] <msafile1> <msafile2> with desired options-h for help (not --help or --version, which are unsupported)--amino, --dna, or --rna