skills/phylogenetics/scripts/phylogenetic_analysis.py

• check_dependencies · function · L22-L39 — def check_dependencies()
• count_sequences · function · L42-L45 — def count_sequences(fasta_file: str) -> int
• run_mafft · function · L48-L76 — def run_mafft(input_fasta: str, output_fasta: str, n_threads: int = 4, method: str = "auto") -> str
• run_iqtree · function · L79-L115 — def run_iqtree(aligned_fasta: str, prefix: str, seq_type: str = "nt", bootstrap: int = 1000, n_threads: int = 4, outgroup: str = None) -> str
• run_fasttree · function · L118-L134 — def run_fasttree(aligned_fasta: str, output_tree: str, seq_type: str = "nt") -> str
• visualize_tree · function · L137-L173 — def visualize_tree(tree_file: str, output_png: str, outgroup: str = None) -> None
• tree_summary · function · L176-L203 — def tree_summary(tree_file: str) -> dict
• main · function · L206-L268 — def main()