Agent skill · research science · aiskillstore
busco-phylogeny
Generate phylogenies from genome assemblies using BUSCO/compleasm-based single-copy orthologs with scheduler-aware workflow generation
Why this skill is useful
Adds multiple executable scripts for phylogenetic analysis and scheduler-specific workflow generation that are not commonly found in public documentation.
What it needs
Requires bioconda, docker installed locally. About 10k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
BUSCO-based Phylogenomics Workflow Generator This skill provides phylogenomics expertise for generating comprehensive, scheduler-aware workflows for phylogenetic inference from genome assemblies using single-copy orthologs. Purpose This skill helps users generate phylogenies from genome assemblies by: 1. Handling mixed input (local files and NCBI accessions) 2. Creating scheduler-specific scripts (SLURM, PBS, cloud, local) 3. Setting up complete workflows from raw genomes to final trees 4. Providing quality control and recommendations 5. Supporting flexible software management (bioconda, Docker, custom) Available Resources The skill provides access to these bundled resources: Scripts (scripts/) queryncbiassemblies.py - Query NCBI for available genome assemblies by taxon name (new!) downloadncbigenomes.py - Download genomes from NCBI using BioProjects or Assembly accessions renamegenomes.py - Rename genome files with meaningful sample names (important!) generateqcreport.sh - Generate quality control reports from compleasm results extractorthologs.sh - Extract and reorganize single-copy orthologs runaliscore.sh - Wrapper for Aliscore to identify randomly similar sequences (RSS) runalicut.sh - Wrapper for ALICUT to remove RSS positions from alignments runaliscorealicutbatch.sh - Batch process all alignments through Aliscore + ALICUT convertfasconcattopartition.py - Convert FASconCAT output to IQ-TREE partition format predownloadedaliscorealicut/ - Pre-tested Aliscore and ALICUT Perl scripts Templates (templates/) slurm/ - SLURM job scheduler templates pbs/ - PBS/Torque job scheduler templates local/ - Local machine templates (with GNU parallel) README.md - Complete template documentation References (references/) REFERENCE.md - Detailed technical reference including: Sample naming best practices BUSCO lineage datasets (complete list) Resource recommendations (memory, CPUs, walltime) Detailed step-by-step implementation guides Quality control guidelines Aliscore/ALICUT d …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/busco-phylogeny