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bio-alignment-multiple
82 / 100 · Low risk
Fine to try.
By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c
Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.
Works with any agent that supports SKILL.md skills.
What this skill can do
Runs commands on your computer
This is disclosed by the author in the skill's SKILL.md or README.
Found in 21 places.
Show 17 more
- skills/bio-alignment-multiple/SKILL.md, line 199
mafft --add new_seqs.fasta existing_alignment.fasta > updated.fasta - skills/bio-alignment-multiple/SKILL.md, line 223
muscle -align input.fasta -output aligned.fasta -threads 8 - skills/bio-alignment-multiple/SKILL.md, line 237
muscle -super5 input.fasta -stratified -output ensemble.efa - skills/bio-alignment-multiple/SKILL.md, line 254
clustalo -i input.fasta -o aligned.fasta --auto - skills/bio-alignment-multiple/SKILL.md, line 290
t_coffee input.fasta -output fasta_aln -outfile aligned.fasta - skills/bio-alignment-multiple/SKILL.md, line 324
mafft --localpair --maxiterate 1000 proteins.fasta > proteins_aligned.fasta - skills/bio-alignment-multiple/SKILL.md, line 332
pal2nal.pl proteins_aligned.fasta codons.fasta -output paml -codontable 2 > codons_mt.phy - skills/bio-alignment-multiple/SKILL.md, line 344
prank -d=codons.fasta -o=prank_aligned -codon -F - skills/bio-alignment-multiple/SKILL.md, line 367
java -jar macse_v2.jar -prog alignSequences -seq coding_seqs.fasta \ - skills/bio-alignment-multiple/SKILL.md, line 379
OMM_MACSE_v12.02.sif --in_seq_file orthogroup.fasta --out_dir omm_out --out_file_prefix orthogroup --genetic_code_number 1 - skills/bio-alignment-multiple/SKILL.md, line 387
hyphy pre-msa.bf --input cds.fasta - skills/bio-alignment-multiple/examples/codon_alignment.py, line 13
subprocess.run( - skills/bio-alignment-multiple/examples/codon_alignment.py, line 15
stdout=out, stderr=subprocess.PIPE, check=True - skills/bio-alignment-multiple/examples/codon_alignment.py, line 23
subprocess.run( - skills/bio-alignment-multiple/examples/codon_alignment.py, line 25
stdout=out, stderr=subprocess.PIPE, check=True - skills/bio-alignment-multiple/examples/run_msa.py, line 19
subprocess.run(cmd, stdout=out, stderr=subprocess.PIPE, check=True) - skills/bio-alignment-multiple/examples/run_msa.py, line 27
subprocess.run(cmd, check=True)
and 1 more places
Downloads and installs other software
The author does not mention this.
Found in 1 place.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'bio-alignment-multiple' ] || [ -L ~/.agents/skills/'bio-alignment-multiple' ]; then echo 'A skill folder named bio-alignment-multiple already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-alignment-multiple' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-alignment-multiple' ~/.agents/skills/'bio-alignment-multiple' && rm -rf "$d"; fi
Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-alignment-multiple' ~/.claude/skills/'bio-alignment-multiple' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.
Badge for your README
The badge for lilinji/GeneTind-Life-Skills shows the score of its lowest-scoring skill.

[](https://zalavijaysinh.github.io/skilltrust/repos/lilinji/GeneTind-Life-Skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-11 | 908229c | 82 |