Thinking Deeply

8

brunoasm

Engages structured analysis to explore multiple perspectives and context dependencies before responding. Use when users ask confirmation-seeking questions, make leading statements, request binary choices, or when feeling inclined to quickly agree or disagree without thorough consideration.

busco-phylogeny

8

brunoasm

Generate phylogenies from genome assemblies using BUSCO/compleasm-based single-copy orthologs with scheduler-aware workflow generation

biogeobears

8

brunoasm

Set up and execute phylogenetic biogeographic analyses using BioGeoBEARS in R. Use when users request biogeographic reconstruction, ancestral range estimation, or want to analyze species distributions on phylogenies. Handles input file validation, data reformatting, RMarkdown workflow generation, and result visualization.

extract-from-pdfs

8

brunoasm

This skill should be used when extracting structured data from scientific PDFs for systematic reviews, meta-analyses, or database creation. Use when working with collections of research papers that need to be converted into analyzable datasets with validation metrics.