Data for: Positive selection on the nad4 gene in Ophiocordycipitaceae — convergent evidence from multi-method analysis

This dataset supports the manuscript "Positive selection on the nad4 gene in Ophiocordycipitaceae — convergent evidence from multi-method analysis" submitted to Gene. It contains the complete analytical workflow for detecting positive selection on the mitochondrial nad4 gene across 16 taxa of Ophiocordycipitaceae. Contents: • Codon-aware multiple sequence alignment of nad4 in PHYLIP, FASTA, and NEXUS formats (1,614 bp, 538 codons) • Neighbor-Joining phylogenetic trees in Newick format • PAML codeml output files for M0 (one-ratio), M7 (beta), and M8 (beta+ω) site models, including corresponding control (.ctl) files • Datamonkey server results (FEL, MEME, FUBAR) • Seven Python scripts for alignment processing, PAML execution, and comparative analysis Methods summary: Positive selection was assessed using three complementary approaches: (1) PAML codeml site models with likelihood ratio tests (M7 vs M8), (2) Datamonkey web server (FEL, MEME, FUBAR), and (3) physicochemical property divergence analysis. Convergent evidence across methods supports positive selection acting on specific codon sites within the nad4 gene.