Evolutionary history of the Hymenoptera - Supplementary Datasets

Data deposited for the paper:
Evolutionary history of the Hymenoptera

1) Folder name:
1-Gene-MSAs_after-pal2nal

Kind of data:
Multiple sequence alignments of orthologous genes after alignment refinement (aa and nt data).

2) Folder name:
2-Main-dataset_dataBlocks-PartitionfinderResults-Final-supermatrix

Kind of data and file formats:
• Main data set: Concatenated supermatrices after the Aliscore and Mare step. Sites have been rearranged according to clan, Pfam-A, Pfam-B and void data blocks. Files are in phylip format.
• Corresponding data block files are given as text files. Data blocks and the supermatices are used as input for the PartitionFinder analysis.
• Results of the PartitionFinder analysis: Best partitioning scheme in RAxML partition file format.
• Files that contain the word “reduced” in their name are the alignment and partition file produced by RAxML when automatically filtering alignment sites, which contain only gap and ambiguous characters.
• All above files are given for aa and nt data sets.

3) Folder name:
3-datasets_decisive-datasets

Kind of data and file formats:
As in number 2) but for the data sets reduced to the decisive data sets. That is, data blocks with missing data in required taxonomic groups has been removed. Decisive data sets are: Aculeata-decisive-dataset, Apoidea-decisive-dataset, Backbone-decisive-dataset.

4) Folder name:
4-datasets_FCLM_and_permutations

Kind of data and file formats:
Data sets used for the Four Cluster Likelihood Mapping method. Files include the partition files in RAxML Format, the taxonomic group files as well as the necessary data sets from which the permutations have been generated. For detail on the methods and the purpose of the permutation test see the Supplemental Experimental Procedures (available online). The generating scripts for the permuted data sets are available upon request. Permuted data sets can also be created by following the description in the Supplemental Experimental Procedures. The reduced matrix is the matrix that was used as input in the permutation script.

5) Folder name:
5-results_rogue_taxa_analyses

Kind of data and file formats:
Result files of the program RogueNaRok for different parameters. Results are given for the analyses conducted for the aa and the nt data sets.

6) Folder name:
6-results_tree_reconstruction_decisive_datasets

Kind of data and file formats:
Resulting phylogenetic trees in Newick format for the decisive data sets.

7) Folder name:
7-results_FCLM_and_permutations

Kind of data and file formats:
Result files of the FCLM analysis. Files are graphic files in the SVG format.

8) Folder name:
8-results_tree-reconstruction_main_analysis

Kind of data and file formats:
Resulting phylogenetic trees in Newick format of the main analysis.

9) Folder name:
9-dating_dataset_and_results

Kind of data and file formats:
Input and result files of the dating analysis.

本数据集为论文《膜翅目演化历史》（Evolutionary history of the Hymenoptera）配套存档数据。

1) 文件夹名称：1-Gene-MSAs_after-pal2nal
数据类型：经比对优化后的直系同源基因多序列比对（Multiple Sequence Alignment, MSA）数据，涵盖氨基酸（amino acid, aa）与核苷酸（nucleotide, nt）两类序列文件。

2) 文件夹名称：2-Main-dataset_dataBlocks-PartitionfinderResults-Final-supermatrix
数据类型与文件格式：
• 核心数据集：经Aliscore与Mare步骤过滤后的串联超级矩阵，序列位点已按蛋白家族类群、Pfam-A、Pfam-B及无数据区块进行重排，文件格式为phylip格式。
• 配套数据区块文件：以文本文件形式提供，数据区块与超级矩阵可作为PartitionFinder分析的输入文件。
• PartitionFinder分析结果：以RAxML分区文件格式存储的最优分区方案。
• 文件名含“reduced”的文件：为RAxML自动过滤比对位点后生成的比对与分区文件，仅包含缺失字符与歧义字符。
• 上述所有文件均对应氨基酸与核苷酸两类数据集。

3) 文件夹名称：3-datasets_decisive-datasets
数据类型与文件格式：
同2)的数据集结构，但仅保留经过筛选的决定性数据集。即移除了在指定分类类群中存在数据缺失的数据区块。决定性数据集包括：Aculeata-decisive-dataset、Apoidea-decisive-dataset、Backbone-decisive-dataset。

4) 文件夹名称：4-datasets_FCLM_and_permutations
数据类型与文件格式：
用于四聚类似然映射（Four Cluster Likelihood Mapping, FCLM）方法的数据集。文件包含RAxML格式的分区文件、分类类群文件，以及用于生成置换测试的原始数据集。有关置换测试的方法与用途详情，请参见补充实验方法（可在线获取）。置换数据集的生成脚本可按需获取，也可根据补充实验方法中的描述自行生成。简化矩阵为置换脚本的输入矩阵。

5) 文件夹名称：5-results_rogue_taxa_analyses
数据类型与文件格式：
不同参数设置下RogueNaRok程序的分析结果文件，涵盖氨基酸与核苷酸两类数据集的分析结果。

6) 文件夹名称：6-results_tree_reconstruction_decisive_datasets
数据类型与文件格式：
决定性数据集对应的系统发育树结果，文件格式为Newick格式。

7) 文件夹名称：7-results_FCLM_and_permutations
数据类型与文件格式：
FCLM分析结果文件，均为可缩放矢量图形（Scalable Vector Graphics, SVG）格式的图像文件。

8) 文件夹名称：8-results_tree-reconstruction_main_analysis
数据类型与文件格式：
主分析对应的系统发育树结果，文件格式为Newick格式。

9) 文件夹名称：9-dating_dataset_and_results
数据类型与文件格式：
分子定年分析的输入文件与结果文件。