Data and Scripts for Reproducing Mitochondrial Phylogenetic Analyses of Alepocephaliformes

This dataset provides the phylogenetic alignments, partition schemes, inferred trees, analytical outputs, statistical test results, and reproducibility scripts associated with a study of mitochondrial genome reconstruction and phylogenetic relationships of Alepocephaliformes. The archive includes maximum-likelihood analyses of amino acid (AA), first- and second-codon-position nucleotide (NT12), and complete codon-position nucleotide (NT123) datasets; Bayesian phylogenetic analyses; approximately unbiased (AU) topology tests; and sensitivity analyses evaluating branch support, model heterogeneity, and missing data. Phylogenetic analyses were conducted using IQ-TREE 3.0.1 and MrBayes 3.2.7a. Original analysis logs and results are provided alongside scripts for computational reproduction. The scripts have been checked for syntax and input-file availability but have not undergone complete computational re-execution. GenBank accession numbers, voucher information, and references for the mitochondrial sequences used in the study are provided in Supplementary Table S1, included in the archive. The README file documents the organization of the dataset, analytical procedures, and reproducibility considerations.