esl-alimask

name	esl-alimask
description	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.
disable-model-invocation	true
user-invocable	true

esl-alimask

Quick Start

• Command: esl-alimask [options] <msafile> ...
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-alimask
• Detailed reference: See references/help.md for full option list and usage details

When To Use This Tool

• Use esl-alimask when you need to remove or retain alignment columns based on an explicit mask, coordinate range, gap fraction, posterior probability, or RF annotation.
• It is appropriate for MSA cleanup before HMM building, consensus trimming, or downstream comparative analyses.
• Use -t for coordinate-based trimming, -g for gap-based masking, and -p for posterior-probability-based masking.
• Reach for --rf-is-mask when the alignment already carries a trusted #=GC RF annotation defining the columns to keep.

Common Patterns

# 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

Recommended Workflow

1. Prepare your MSA file in a supported format (e.g., Stockholm, aligned FASTA)
2. Choose a masking strategy: external mask file, gap-based, posterior probability-based, or RF annotation
3. Run esl-alimask with the appropriate mode flag (-t, -g, -p, or --rf-is-mask) or provide a mask file
4. Verify the output alignment has the expected columns masked or truncated

Guardrails

• Use -h for help; --help and --version are not supported options
• Ensure the MSA file format matches the expected input (check with Easel tools if needed)
• When using -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