Data for Phylogenomics of Auchenorrhyncha (Insecta: Hemiptera) using Transcriptomes: Examining Controversial Relationships via Degeneracy Coding and Interrogation of Gene Conflict

The data in this directory corresponds to: Skinner, R.K., Dietrich, C.H., Walden, K.K.O., Gordon, E., Sweet, A.D., Podsiadlowski, L., Petersen, M., Simon, C., Takiya, D.M., and Johnson, K.P. Phylogenomics of Auchenorrhyncha (Insecta: Hemiptera) using Transcriptomes: Examining Controversial Relationships via Degeneracy Coding and Interrogation of Gene Conflict. Systematic Entomology. Correspondance should be directed to: Rachel K. Skinner, [e-mail] If you use these data, please cite our paper in Systematic Entomology. The following files can be found in this dataset: Amino_acid_concatenated_alignment.phy: the amino acid alignment used in this analysis in phylip format. Amino_acid_raxml_partitions.txt (for reference only): the partitions for the amino acid alignment, but a partitioned amino acid analysis was not performed in this study. Amino_acid_concatenated_tree.newick: the best maximum likelihood tree with bootstrap values in newick format. ASTRAL_input_gene_trees.tre: the concatenated gene tree input file for ASTRAL README_pie_charts.md: explains the the scripts and data needed to recreate the pie charts figure from our paper. There is also another Corresponds to the following files: ASTRAL_species_tree_EN_only.newick: the species tree with only effective number (EN) annotation ASTRAL_species_tree_pp1_only.newick: the species tree with only the posterior probability 1 (main topology) annotation ASTRAL_species_tree_q1_only.newick: the species tree with only the quartet scores for the main topology (q1) ASTRAL_species_tree_q2_only.newick: the species tree with only the quartet scores for the first alternative topology (q2) ASTRAL_species_tree_q3_only.newick: the species tree with only the quartet scores for the second alternative topology (q3) print_node_key_files.py: script needed to create the following files: node_keys.key: text file with node IDs and topologies complete_q_scores.key: text file with node IDs multiplied q scores EN_node_vals.key: text file with node IDs and EN values create_pie_charts_tree.py: script needed to visualize the tree with pie charts, pp1, and EN values plotted at nodes ASTRAL_species_tree_full_annotation.newick: the species tree with full annotation from the ASTRAL analysis. NOTE: It may be more useful to examine individual value files if you want to visualize the tree, e.g., in figtree, since the full annotations are extensive and can make viewing difficult. Complete_NT_concatenated_alignment.phy: the nucleotide alignment that includes unmodified third codon positions. The alignment is in phylip format. Complete_NT_raxml_partitions.txt: the raxml-style partition file of the nucleotide partitions Complete_NT_concatenated_tree.newick: the best maximum likelihood tree from the concatenated complete analysis NT with bootstrap values in newick format Complete_NT_partitioned_tree.newick: the best maximum likelihood tree from the partitioned complete NT analysis with bootstrap values in newick format Degeneracy_coded_nt_concatenated_alignment.phy: the degeneracy coded nucleotide alignment in phylip format Degeneracy_coded_nt_raxml_partitions.txt: the raxml-style partition file for the degeneracy coded nucleotide alignment Degeneracy_coded_nt_concatenated_tree.newick: the best maximum likelihood tree from the degeneracy-coded concatenated analysis with bootstrap values in newick format Degeneracy_coded_nt_partitioned_tree.newick: the best maximum likelihood tree from the degeneracy-coded partitioned analysis with bootstrap values in newick format count_ingroup_taxa.py: script that counts the number of ingroup and/or outgroup taxa present in an alignment

本目录中所含数据对应于：Skinner, R.K.，Dietrich, C.H.，Walden, K.K.O.，Gordon, E.，Sweet, A.D.，Podsiadlowski, L.，Petersen, M.，Simon, C.，Takiya, D.M.，及Johnson, K.P. 发表的《基于转录组学分析Auchenorrhyncha（昆虫纲半翅目）的谱系地理学：通过冗余编码和基因冲突探究争议性关系》。相关信件请寄至：Rachel K. Skinner，[e-mail]。若您使用这些数据，请在《系统昆虫学》杂志中引用我们的论文。本数据集中包含以下文件：
Amino_acid_concatenated_alignment.phy：分析中使用的氨基酸比对，格式为phylip。
Amino_acid_raxml_partitions.txt（仅供参考）：氨基酸比对的分区，但本研究未进行分区氨基酸分析。
Amino_acid_concatenated_tree.newick：新ick格式下最佳最大似然树，包含自举值。
ASTRAL_input_gene_trees.tre：用于ASTRAL的连续基因树输入文件。
README_pie_charts.md：解释了重绘论文中饼图所需的脚本和数据。
此外，还包括以下文件：
ASTRAL_species_tree_EN_only.newick：仅包含有效数量（EN）注释的物种树
ASTRAL_species_tree_pp1_only.newick：仅包含后验概率1（主要拓扑结构）注释的物种树
ASTRAL_species_tree_q1_only.newick：仅包含主要拓扑结构（q1）四重分数的物种树
ASTRAL_species_tree_q2_only.newick：仅包含第一替代拓扑结构（q2）四重分数的物种树
ASTRAL_species_tree_q3_only.newick：仅包含第二替代拓扑结构（q3）四重分数的物种树
print_node_key_files.py：用于创建以下文件的脚本：
node_keys.key：包含节点ID和拓扑结构的文本文件
complete_q_scores.key：包含节点ID和乘积q分数的文本文件
EN_node_vals.key：包含节点ID和EN值的文本文件
create_pie_charts_tree.py：用于将饼图、后验概率1和EN值绘制在节点上的可视化树脚本
ASTRAL_species_tree_full_annotation.newick：包含ASTRAL分析完整注释的物种树。
注意：如果想要可视化树，例如在figtree中查看，单独的值文件可能更有用，因为完整的注释内容繁复，可能会造成观看困难。
Complete_NT_concatenated_alignment.phy：包含未修饰第三密码子位置的核苷酸比对，格式为phylip。
Complete_NT_raxml_partitions.txt：核苷酸分区的raxml风格分区文件
Complete_NT_concatenated_tree.newick：连续完整分析NT最佳最大似然树，新ick格式下包含自举值。
Complete_NT_partitioned_tree.newick：分区完整NT分析最佳最大似然树，新ick格式下包含自举值。
Degeneracy_coded_nt_concatenated_alignment.phy：冗余编码核苷酸比对，格式为phylip。
Degeneracy_coded_nt_raxml_partitions.txt：冗余编码核苷酸比对raxml风格分区文件
Degeneracy_coded_nt_concatenated_tree.newick：冗余编码连续分析最佳最大似然树，新ick格式下包含自举值。
Degeneracy_coded_nt_partitioned_tree.newick：冗余编码分区分析最佳最大似然树，新ick格式下包含自举值。
count_ingroup_taxa.py：用于统计比对中包含的物种群和/或外群物种数量的脚本。