Main data repository for "Comparative analysis of mitochondrial proteomes across the tree of life"

This repository contains the input and processed datasets used in the study “Comparative analysis of mitochondrial proteomes across the tree of life”, as part of the MitoCarta Tree of Life (MitoTOL) project. The dataset spans 673 eukaryotic species (including 203 representative eukaryotes) and 34 prokaryotic groups, and supports analyses of mitochondrial protein evolution, orthogroup inference, ancestral reconstructions, and eukaryogenesis timing. ----- The archive includes: alignments_and_initial_trees.tar.xz — Protein fasta files, multiple sequence alignments, and maximum-likelihood phylogenies for each orthogroup selected for phylogenetic analysis. data.tar.xz — Primary datasets organized by analysis type, including orthogroups, phylogenetically-resolved orthogroups, DeepLoc2.0-mito training datasets and predictions, taxonomic metadata, HGT inferences, ancestral reconstructions, and other analyses. pruned_rooted_trees.tar.xz — Pruned and rooted trees used for downstream phylogenomic analyses. reconciled_consensus_trees_branch_length_optimization_with_supports_species.tree.[1-6].tar.xz — Reconciled consensus protein trees with optimized branch lengths and node support values, under six species tree topologies. reconciled_consensus_trees_for_timing_species.tree.[1-6].tar.xz — Reconciled consensus protein trees with optimized branch lengths and labeled ancestral nodes for timing analyses, under six species tree topologies. reconciled_trees_posterior_clades_species.tree.[1-6].tar.xz — Clade frequency tables for posterior samples of reconciled trees, under six species tree topologies. reconciled_trees_species.tree.[1-6].tar.xz — AleRax reconciliation outputs, including posterior samples of reconciled trees and majority-rule consensus trees, under six species tree topologies. species_fastas.tar.xz — Protein fasta files for all eukaryotic species and prokaryotic groups included in the study. ----- All datasets follow consistent naming conventions (e.g., [Orthogroup_ID], [PhROG_ID], [TAXONOMY_ID]). Detailed documentation of file contents is provided in the accompanying README.txt. The full computational workflow, including scripts for alignment, tree inference, reconciliation, and ancestral reconstructions, is available at:https://github.com/michaelzhuchen/mito-evolution