VEHoP: A Versatile, Easy-to-use, and Homology-based Phylogenomic pipeline accommodating diverse sequences

Supplementary data for "Reliable inference of phylogenomic relationship via assembly-based strategy accommodating raw reads and proteins", including: initial assembly results of the used datasets, the generated supermatrix, and original tree files.This attachment contains analysis results related to the Oyster dataset, with details of each file/folder as follows:Data_size_1G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 1G. It includes assembly results, supermatrix files, and partition information files for this data volume.Data_size_2G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 2G. It includes assembly results, supermatrix files, and partition information files for this data volume.Data_size_4G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 4G. It includes assembly results, supermatrix files, and partition information files for this data volume.Data_size_6G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 6G. It includes assembly results, supermatrix files, and partition information files for this data volume.Data_size_8G folder: Corresponds to the analysis results of the Oyster dataset when subsampled to 8G. It includes assembly results, supermatrix files, and partition information files for this data volume.Full-size folder: Corresponds to the analysis results of the complete Oyster dataset. It contains: high-quality genome protein files (and their matching matrices & partition files); full-volume next-generation sequencing data (plus the corresponding matrix & partition files); and RNA dataset files.tree_files folder: Contains phylogenetic tree files constructed based on analysis results of the Oyster dataset (covering all data volumes).Mollusca.six.fasta file: A FASTA-format protein alignment file used in this Oyster dataset analysis, containing 6 sequences of the Mollusca group (file size: 67,095 KB).