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Run npx skillmds add vimalinx/esl-alimask in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

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Is Esl Alimask free to use?

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Who published Esl Alimask?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Esl Alimask by vimalinx — Agent Skill

Name: Esl Alimask
Rating: 4.2 (5 reviews)
Author: vimalinx

Esl Alimask

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.

vimalinx c9bc491 2 files · 3.6 KB Updated Sep 9, 2026 0 repo stars

File contents

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

Prepare your MSA file in a supported format (e.g., Stockholm, aligned FASTA)
Choose a masking strategy: external mask file, gap-based, posterior probability-based, or RF annotation
Run esl-alimask with the appropriate mode flag (-t, -g, -p, or --rf-is-mask) or provide a mask file
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

---name: esl-alimaskdescription: 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 ## 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 ```bash # 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

Frequently asked questions