← All skills
busco-phylogeny
90 / 100 · Low risk
Fine to try. Some of what it can do is expected: a productivity skill usually connects to your mail, calendar or notes.
By boisenoise/skills-collections (GitHub) · productivity · 12 stars · scanned at commit 419c39f
Generate phylogenies from genome assemblies using BUSCO/compleasm-based single-copy orthologs with scheduler-aware workflow generation
Works with any agent that supports SKILL.md skills.
What this skill can do
Runs commands on your computer
The author does not mention this.
Found in 18 places.
Show 15 more
- skills/brunoasm-phylo_from_buscos/SKILL.md, line 393
python scripts/download_ncbi_genomes.py --bioprojects PRJNA12345 -o genomes.zip - skills/brunoasm-phylo_from_buscos/SKILL.md, line 399
python scripts/download_ncbi_genomes.py --assemblies GCA_123456789.1 -o genomes.zip - skills/brunoasm-phylo_from_buscos/SKILL.md, line 442
bash scripts/generate_qc_report.sh qc_report.csv - skills/brunoasm-phylo_from_buscos/SKILL.md, line 461
bash scripts/extract_orthologs.sh LINEAGE_NAME - skills/brunoasm-phylo_from_buscos/SKILL.md, line 474
cd single_copy_orthologs/unaligned_aa - skills/brunoasm-phylo_from_buscos/SKILL.md, line 514
conda activate phylo # Has Perl installed - skills/brunoasm-phylo_from_buscos/SKILL.md, line 524
python ../scripts/convert_fasconcat_to_partition.py FcC_info.xls partition_def.txt - skills/brunoasm-phylo_from_buscos/SKILL.md, line 550
iqtree -s FcC_supermatrix.fas -spp partition_search.best_scheme.nex \ - skills/brunoasm-phylo_from_buscos/SKILL.md, line 572
conda activate phylo - skills/brunoasm-phylo_from_buscos/scripts/download_ncbi_genomes.py, line 35
result = subprocess.run(cmd, check=True, capture_output=True, text=True) - skills/brunoasm-phylo_from_buscos/scripts/download_ncbi_genomes.py, line 40
except subprocess.CalledProcessError as e: - skills/brunoasm-phylo_from_buscos/scripts/download_ncbi_genomes.py, line 69
result = subprocess.run(cmd, check=True, capture_output=True, text=True) - skills/brunoasm-phylo_from_buscos/scripts/download_ncbi_genomes.py, line 88
except subprocess.CalledProcessError as e: - skills/brunoasm-phylo_from_buscos/scripts/query_ncbi_assemblies.py, line 83
result = subprocess.run( - skills/brunoasm-phylo_from_buscos/scripts/query_ncbi_assemblies.py, line 154
except subprocess.CalledProcessError as e:
Sends data to these websites: iqtree.github.io, raw.githubusercontent.com, github.com
The author does not mention this. Expected for a productivity skill.
Found in 17 places.
Show 14 more
- skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 771
wget -q "${GITHUB_BASE}/ALICUT_V2.31.pl" -O scripts/ALICUT_V2.31.pl && \ - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 772
wget -q "${GITHUB_BASE}/Aliscore_module.pm" -O scripts/Aliscore_module.pm; then - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 785
if wget -q https://github.com/PatrickKueck/AliCUT/raw/master/Aliscore_v.2.0/Aliscore.02.2.pl -O scripts/Aliscore.02.2.pl && \ - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 786
wget -q https://github.com/PatrickKueck/AliCUT/raw/master/ALICUT_V2.3.1/ALICUT_V2.31.pl -O scripts/ALICUT_V2.31.pl && \ - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 787
wget -q https://github.com/PatrickKueck/AliCUT/raw/master/Aliscore_v.2.0/Aliscore_module.pm -O scripts/Aliscore_module.pm; then - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 934
wget https://raw.githubusercontent.com/PatrickKueck/AliCUT/master/Aliscore.02.2.pl - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 935
wget https://raw.githubusercontent.com/PatrickKueck/AliCUT/master/Aliscore_module.pm - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 938
wget https://raw.githubusercontent.com/PatrickKueck/AliCUT/master/ALICUT_V2.31.pl - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 998
wget https://raw.githubusercontent.com/PatrickKueck/FASconCAT-G/master/FASconCAT-G_v1.06.1.pl - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 1045
wget https://github.com/iqtree/iqtree2/releases/download/v2.3.6/iqtree-2.3.6-Linux-intel.tar.gz - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 1070
wget https://github.com/iqtree/iqtree2/releases/download/v2.3.6/iqtree-2.3.6-macOS-intel.tar.gz - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 1095
wget https://github.com/iqtree/iqtree2/releases/download/v2.3.6/iqtree-2.3.6-macOS-arm.tar.gz - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 1133
wget https://github.com/smirarab/ASTRAL/raw/master/Astral.5.7.8.zip - skills/brunoasm-phylo_from_buscos/references/REFERENCE.md, line 1303
wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'busco-phylogeny' ] || [ -L ~/.agents/skills/'busco-phylogeny' ]; then echo 'A skill folder named busco-phylogeny already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/boisenoise/skills-collections' "$d" && git -C "$d" checkout --quiet '419c39fde874b8baecbb36a397b967e0190a2ece' -- 'skills/brunoasm-phylo_from_buscos' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/brunoasm-phylo_from_buscos' ~/.agents/skills/'busco-phylogeny' && 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/'busco-phylogeny' ~/.claude/skills/'busco-phylogeny' (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 boisenoise/skills-collections shows the score of its lowest-scoring skill.

[](https://zalavijaysinh.github.io/skilltrust/repos/boisenoise/skills-collections/)
Score history
| Date | Version | Score |
|---|
| 2026-11-12 | 419c39f | 90 |
| 2026-11-08 | 5fe45e5 | 90 |
| 2026-11-06 | b89b2f5 | 90 |