Data from: Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Alignments- Concatenated nucleotide alignment - Concatenated protein alignment - 1,105 exon alignments (protein and nucleotide) - 1,721 exon alignments, with all nHmmer hits aligned - 616 exon alignments of discarded loci, with only the best hit per locus -8-model-species-alignmentsTreeFilesSee Appendix 1 in the Supplementary Appendix for the correspondence between these tree files and the figures in the paper.GGI-Constraint-TreesMaster constraint trees for all hypotheses tested. See Arcila et al. 2017 for a full tutorial of the GGI method.ScriptsScripts used to extract markers from genomes/transcriptomes. There is a short tutorial included in the zip archive that explains the pipeline. Scripts are provided without warranty.MCMCTreeFilesFiles for running divergence time estimation in MCMCTree. See Supplementary Appendix for list of fossil calibrations and details on our three calibration schemes.BGI-Sequencing-ResultsAssembly metrics from BGI-sequenced transcriptomes for Fish T1K

比对集：
1. 串联核苷酸比对序列
2. 串联蛋白质比对序列
3. 1105组外显子（exon）比对（涵盖蛋白质与核苷酸两类比对）
4. 1721组外显子比对，所有nHmmer搜索命中结果均已完成比对
5. 616组经剔除位点的外显子比对，每个位点仅保留最优比对结果
6. 8个模式物种比对集
树文件：请参阅补充附录中的附录1，以明确本部分树文件与论文附图的对应关系。
GGI约束树：所有待验证假说的主约束树。有关GGI方法的完整教程可参考Arcila等人2017年的研究成果。
脚本：用于从基因组/转录组中提取标记基因的脚本。压缩包内附带一份简短教程，对分析流程进行详细说明。本脚本未附带任何形式的担保。
MCMCTree文件：用于在MCMCTree中开展分化时间估算的相关文件。请参阅补充附录，了解化石校准点列表以及我们采用的三种校准方案的具体细节。
BGI测序结果：来自BGI测序的鱼类T1K转录组的组装统计数据。