Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.

READMEDescription of files contained within this repositoryComplete_Sequence_Files-contains .phy files for all 498 loci and 326 sequences (two alleles per individual) -concatenated.phy contains sequences for all 498 loci together -species-consensus.phy contains concatenated sequence for the species-level consensusesOnePer_Sequence_Files-contains .phylip files for all 498 loci and 65 taxa (one sequence per taxon) -T74_Concat_OnePer.phy contains sequences for all 498 loci togetherConsensus_Sequence_Files-contains .phy files for all 498 loci and 65 taxa based on species-leel consensus -consensus.phy contains sequences for all 498 loci togetherReduced_Sequence_Files-contains .phy files for subset of 354 loci and 60 taxaTree_Files-Astral_Bootstrap.tre newick formatted 100 bootstrap replicates from the COMPLETE ASTRAL-II species analysis -Gene_Trees_Full.tre newick formatted 498 "best" gene trees from RAxML (in ascending order) -Gene_Trees_Reduced.tre newick formatted reduced 354 "best" gene trees form RAxML (in ascending order) -Individual_Trees.tre newick formatted trees based on 326 sequences to check for monophyly -RAxML_Bootstrap.tre -neewick formatted bootstrap replicates from the RAxML species analysis -Species_Trees_Complete.tre newick formatted species trees (ASTRAL-II and SVDquartets) with support values for all 65 taxa, 498 loci (COMPLETE dataset) -Species_Trees_Consensus.tre newick formatted species trees generated using the CONSENSUS dataset -Species_Trees_OnePer.tre newick formatted species trees generated using the ONEPER dataset -Species_Trees_Reduced.tre newick formatted species trees with support values for REDUCED set of 60 taxa, 354 loci -Species_Trees_Schnitzler.tre newick formatted species trees with species and data from Schnitzler et al. included (AUGMENTED dataset) -SVD_bootstrap.tre newick formatted 100 bootstrap replicates from the SVDquartets species analysisDistancescontains pairwise distances among gene trees, among species trees, and between gene trees (observed, randomly generated, and simulated using COAL)Internode_Certaintyfor all four species trees, contains internode certainty and internode certainty all values from RAxML, along with branch lengthsLocus_Infomatches Table 2 in manuscript, contains information on all loci, including length, parsimony informative sites, and distance to species trees.

## 本仓库包含文件说明
1. **Complete_Sequence_Files**：内含所有498个基因座、326条序列（每个个体对应两个等位基因）的.phy格式序列文件。其中：
- `concatenated.phy`：包含全部498个基因座的拼接序列
- `species-consensus.phy`：包含物种水平共识序列的拼接结果
2. **OnePer_Sequence_Files**：内含所有498个基因座、65个分类单元（每个分类单元仅一条序列）的.phylip格式序列文件。其中：
- `T74_Concat_OnePer.phy`：包含全部498个基因座的拼接序列
3. **Consensus_Sequence_Files**：基于物种水平共识构建的、包含所有498个基因座与65个分类单元的.phy格式序列文件。其中：
- `consensus.phy`：包含全部498个基因座的拼接序列
4. **Reduced_Sequence_Files**：内含354个基因座与60个分类单元子集的.phy格式序列文件
5. **Tree_Files**：各类系统发育树文件：
- `Astral_Bootstrap.tre`：Newick格式的100次自举重复分析结果，源自完整ASTRAL-II物种树分析
- `Gene_Trees_Full.tre`：Newick格式的498棵最优基因树，由RAxML生成并按升序排列
- `Gene_Trees_Reduced.tre`：Newick格式的354棵精简最优基因树，由RAxML生成并按升序排列
- `Individual_Trees.tre`：Newick格式的系统发育树，基于326条序列构建，用于检验单系性
- `RAxML_Bootstrap.tre`：Newick格式的RAxML物种树分析自举重复结果
- `Species_Trees_Complete.tre`：Newick格式的物种树（包含ASTRAL-II与SVDquartets两种方法），附带全部65个分类单元、498个基因座的支持值（完整数据集）
- `Species_Trees_Consensus.tre`：Newick格式的物种树，基于共识数据集构建
- `Species_Trees_OnePer.tre`：Newick格式的物种树，基于OnePer数据集构建
- `Species_Trees_Reduced.tre`：Newick格式的物种树，附带精简集（60个分类单元、354个基因座）的支持值
- `Species_Trees_Schnitzler.tre`：Newick格式的物种树，整合了Schnitzler等研究中的物种与数据（增强数据集）
- `SVD_bootstrap.tre`：Newick格式的100次自举重复分析结果，源自SVDquartets物种树分析
6. **Distances**：内含基因树间、物种树间以及基因树与物种树间的成对距离数据，涵盖观测值、随机生成值以及通过COAL模拟得到的数值
7. **Internode_Certainty**：针对四类物种树，包含RAxML输出的节点间确定性与全节点间确定性数值，同时附带分支长度信息
8. **Locus_Info**：对应论文表2，内含所有基因座的相关信息，包括序列长度、简约信息位点数以及与物种树的距离