Phylogenomic data for Herranz et al.

Data for phylotranscriptomic analysis of Kinorhyncha by Herranz et al. The repository contains: 0_OrthoFinder_MultipleSequenceAlignments.tar.gz: orthogroup alignment files as produced from OrthoFinder. 1_OrthoFinder_GeneTrees.tar.gz: gene trees obtained for orthogroup alignments as produced by OrthoFinder using FastTree. 2_OrthoFinder_ResolvedGeneTrees.tar.gz: rooted and resolved gene trees as produced by OrthoFinder. 3a_PhyloTreePruner_SingleCopyAlignments_GeneTrees.tar.gz: Single copy alignments as generated by PhyloTreePruner from the Resolved Gene trees and the Multiple Sequence Alignments. After pruning, alignments were realigned with MAFFT L-ins-i. Gene trees obtained from the realigned single copy gene trees with IQTREE. 3b_ASTRAL_SingleCopySpeciesTree.tar.gz: Input and output files of ASTRAL-III species tree analysis. 3c_IQTREE_Supermatrices.tar.gz: Input and output files of concatenated species tree analysis based on the 70% and 80% occupancy matrix analyzed with IQTREE. 4_ASTRAL-Pro_MultiCopySpeciesTree.tar.gz: Input and output files of ASTRAL-Pro species tree analysis, which analyzed multi copy gene trees from OrthoFinder (1_OrthoFinder_GeneTrees.tar.gz) to build a species tree. 5a_ASTRAL-Pro_noLowQuality.tar.gz: input and output files for ASTRAL-Pro species tree analysis after removing lower quality transcriptomes (E. dujardinii, E. kohni, Pycnophyes sp.). 5b_ASTRAL-Pro_noOutgroups.tar.gz: input and output files for ASTRAL-Pro species tree analysis after removing the transcriptomes of the long branched Nematoida and Loricifera.

本数据集为Herranz等人针对动吻动物门（Kinorhyncha）开展的系统发育转录组学分析所用数据。该数据仓库包含以下文件：
0_OrthoFinder_多序列比对文件.tar.gz：由OrthoFinder生成的同源基因簇比对文件；
1_OrthoFinder_基因树文件.tar.gz：由OrthoFinder借助FastTree生成的、对应同源基因簇比对的基因树；
2_OrthoFinder_已解析基因树文件.tar.gz：由OrthoFinder生成的带根且已解析的基因树；
3a_PhyloTreePruner_单拷贝比对与基因树文件.tar.gz：由PhyloTreePruner基于已解析基因树与多序列比对生成单拷贝比对序列；经序列修剪后，使用MAFFT L-ins-i工具对该单拷贝比对序列进行重比对；随后基于重比对后的单拷贝基因树，通过IQTREE工具构建基因树；
3b_ASTRAL_单拷贝物种树文件.tar.gz：ASTRAL-III物种树分析的输入与输出文件；
3c_IQTREE_超级矩阵文件.tar.gz：基于70%与80%基因存在率矩阵的串联物种树分析的输入与输出文件，该分析由IQTREE执行；
4_ASTRAL-Pro_多拷贝物种树文件.tar.gz：ASTRAL-Pro物种树分析的输入与输出文件，该方法通过分析OrthoFinder生成的多拷贝基因树（即1_OrthoFinder_GeneTrees.tar.gz）以构建物种树；
5a_ASTRAL-Pro_低质量转录组过滤后文件.tar.gz：移除低质量转录组（E. dujardinii、E. kohni、Pycnophyes sp.）后的ASTRAL-Pro物种树分析的输入与输出文件；
5b_ASTRAL-Pro_外类群移除后文件.tar.gz：移除长分支的线虫类（Nematoida）与铠甲动物门（Loricifera）转录组后的ASTRAL-Pro物种树分析的输入与输出文件。