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This skill automates the complex process of building phylogenetic trees from genomic data by leveraging BUSCO or compleasm to identify single-copy orthologs. It guides users through the entire bioinformatics lifecycle—from querying and downloading NCBI assemblies to alignment, trimming, and maximum likelihood tree inference—while providing environment-specific scripts for SLURM, PBS, or local execution. It is particularly useful for researchers needing reproducible, high-throughput workflows that handle everything from quality control to final species tree estimation.
