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.gz — Protein fasta files, multiple sequence alignments, and maximum-likelihood phylogenies for each orthogroup. data.tar.gz — Primary datasets organized by analysis type, including orthogroups, phylogenetically-resolved orthogroups, DeepLoc2.0-mito training datasets and predictions, taxonomic metadata, HGT inferences, and reconstruction outputs. pruned_rooted_trees.tar.gz — Pruned and rooted trees used for downstream phylogenomic analyses. reconciled_consensus_trees_branch_length_optimization_with_supports_species.tree.[1-6].tar.gz — 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.gz — 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.gz — Clade frequency tables for posterior samples of reconciled trees, under six species tree topologies. reconciled_trees_species.tree.[1-6].tar.gz — AleRax reconciliation outputs, including posterior samples of reconciled trees and majority-rule consensus trees, under six species tree topologies. species_fastas.tar.gz — 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 Please cite this dataset using 10.5281/zenodo.20466494本仓库包含研究"生命之树线粒体蛋白质组比较分析"（"Comparative analysis of mitochondrial proteomes across the tree of life"）所使用的输入与处理后数据集，该研究隶属于线粒体蛋白组生命之树（MitoCarta Tree of Life, MitoTOL）项目。本数据集涵盖673个真核生物物种（包含203个代表性真核生物）与34个原核生物类群，可支撑线粒体蛋白质演化、直系同源组（orthogroup）推断、祖先状态重建以及真核生物起源时间测算等分析工作。 该归档文件包含以下内容： 1. alignments_and_initial_trees.tar.gz：对应每个直系同源组的蛋白质FASTA文件、多序列比对结果与最大似然系统发育树。 2. data.tar.gz：按分析类型组织的原始数据集，涵盖直系同源组、系统发育解析直系同源组、DeepLoc2.0线粒体训练数据集与预测结果、分类元数据、水平基因转移（Horizontal Gene Transfer, HGT）推断结果以及重建输出文件。 3. pruned_rooted_trees.tar.gz：用于下游系统发育基因组学分析的修剪并定根的系统发育树。 4. reconciled_consensus_trees_branch_length_optimization_with_supports_species.tree.[1-6].tar.gz：基于6种物种树拓扑结构，带有优化分支长度与节点支持度的协调一致蛋白质树。 5. reconciled_consensus_trees_for_timing_species.tree.[1-6].tar.gz：基于6种物种树拓扑结构，带有优化分支长度并标记祖先节点以用于时间测算分析的协调一致蛋白质树。 6. reconciled_trees_posterior_clades_species.tree.[1-6].tar.gz：基于6种物种树拓扑结构的协调树后验样本支系频率表。 7. reconciled_trees_species.tree.[1-6].tar.gz：AleRax协调树输出结果，包含基于6种物种树拓扑结构的协调树后验样本与多数法则一致性树。 8. species_fastas.tar.gz：本研究纳入的所有真核生物物种与原核生物类群的蛋白质FASTA文件。 所有数据集均遵循统一命名规范（例如[Orthogroup_ID]、[PhROG_ID]、[TAXONOMY_ID]）。文件内容的详细说明见配套的README.txt文档。 完整的计算工作流（包含比对、树推断、树协调以及祖先状态重建的脚本）可通过以下网址获取：https://github.com/michaelzhuchen/mito-evolution 请使用DOI: 10.5281/zenodo.20466494 引用本数据集。