Dating Alphaproteobacteria evolution with eukaryotic fossils

Data and codes for the study Wang, S., Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat Commun 12, 3324 (2021). For a more detailed introduction to each dataset, please see the file Readme.docx. Please let me know should there be any question.<br> <b>host_asr/</b>:
reconstruction of ancestral hosts of<b>phylobayes/:</b>
time estimates using phylobayes<b>beast/:</b>
time estimates using BEAST<b>phylogeny/:</b>
phylogenomic reconstruction of α-proteobacteria+mitochondria with two recoding schemes (<i>dayhoff4</i> and <i>SR4</i>) based on GTR+G+F+C30 under PMSF approximation<b>mcmc3r/:</b>
mcmc3r analysis using the 20-taxon (s20) and 40-taxon (s20) subsets of species<b>dating-dna/:
</b>time estimates using MCMCTree based on nucleotides<b>dating-aa/: </b>time
estimates using MCMCTree based on amino acids. You might wish to note that the tree presented in Fig. 1 corresponds to topo1.<b>dating-expanded/:</b> MCMCTree molecular
clock analysis with the expanded genome set based on amino acids<b>dating-cyano/:</b> MCMCTree molecular clock
analysis using the cyanobacteria-based strategy<b>scripts/:</b> scripts used in analysis

本数据集及配套代码源自Wang S、Luo H发表于《自然-通讯》（*Nature Communications*）2021年第12卷第3324页的研究论文《利用真核化石标定α-变形菌门（Alphaproteobacteria）演化时间》（Dating Alphaproteobacteria evolution with eukaryotic fossils）。各数据集的详细说明请参见Readme.docx文件。如有任何疑问，欢迎垂询。
<b>host_asr/</b>: 祖先宿主重建分析
<b>phylobayes/:</b> 基于PhyloBayes的演化时间估算分析
<b>beast/:</b> 基于BEAST的演化时间估算分析
<b>phylogeny/:</b> 基于PMSF近似下的GTR+G+F+C30模型，采用dayhoff4与SR4两种编码方案，对α-变形菌门+线粒体进行系统基因组学重建
<b>mcmc3r/:</b> 采用20分类群（s20）与40分类群（s20）物种子集开展的mcmc3r分析
<b>dating-dna/:</b> 基于核苷酸序列、采用MCMCTree的演化时间估算分析
<b>dating-aa/: </b>基于氨基酸序列、采用MCMCTree的演化时间估算分析。需注意，本文图1对应的系统发育树为topo1。
<b>dating-expanded/:</b> 基于氨基酸序列、采用扩展基因组数据集开展的MCMCTree分子钟分析
<b>dating-cyano/:</b> 采用基于蓝细菌的策略开展的MCMCTree分子钟分析
<b>scripts/:</b> 分析过程中使用的脚本文件