Use when you need to mask columns in a multiple sequence alignment using gap frequencies, posterior probabilities, external mask files, or the RF annotation, or to truncate alignments to specific coordinate ranges.
esl-alimask [options] <msafile> .../home/vimalinx/miniforge3/envs/bio/bin/esl-alimaskreferences/help.md for full option list and usage detailsesl-alimask when you need to remove or retain alignment columns based on an explicit mask, coordinate range, gap fraction, posterior probability, or RF annotation.-t for coordinate-based trimming, -g for gap-based masking, and -p for posterior-probability-based masking.--rf-is-mask when the alignment already carries a trusted #=GC RF annotation defining the columns to keep.# Keep only columns 23..100 of an alignment
esl-alimask -t alignment.sto 23..100 > trimmed.sto
# Mask columns with too many gaps
esl-alimask -g --gapthresh 0.3 alignment.sto > gapmasked.sto
# Mask using posterior probabilities
esl-alimask -p --pavg 0.9 alignment.sto > ppmasked.sto
# Apply an explicit 0/1 mask file
esl-alimask alignment.sto mask.txt > masked.sto
esl-alimask with the appropriate mode flag (-t, -g, -p, or --rf-is-mask) or provide a mask file-h for help; --help and --version are not supported options-t, provide coordinates in the correct format and range for the alignment-g and -p can be combined, but the other major usage modes are mutually exclusive