# # The following files were used for the analyses of these paper. # 1. The fasta files for the maximum (ML) likelihood phylogenies (for each dataset) ------------------------------------------------------------------------------- DatasetA1_allignament_ITS.fas DatasetA2_actin_allignament.fasta DatasetA2_alliganment_ITS_COX_ACTIN.fas DatasetA2_COX_allignament.fasta DatasetA2_ITS_allignament.fas DatasetF1_allignament_for_HN.fas DatasetF2_allignament_for_HN.fas DatasetF3_allignament_3genes_concatanated.fas DatasetF3_allignament_DEAD.fas DatasetF3_allignament_EF.fas DatasetF3_allignament_ITS.fas DatasetF4_allignament_BTUB.fas DatasetF4_allignament_concatanated.fas DatasetF4_allignament_DEAD.fas DatasetF4_allignament_EF.fas DatasetF4_allignament_IGS.fas DatasetF4_allignament_ITS.fas DatasetF4_allignament_RPB2.fas # 2. The scaffolds obtained from Dibaeis baeomyces, Icmadophila ericetorum, Siphula ceratites and Thamnolia lineage C genomes ------------------------------------------------------------------------------------------------------------------------------ Scaffolds_Dibaeis.txt Scaffolds_Icmadophila.txt Scaffolds_Siphula.txt Scaffolds_Thamnolia.txt # 3. The ML phylogenies for each dataset ---------------------------------------- DatasetA1_tree.tre DatasetA2_tree.tre DatasetF4_BTUB_tree.tre DatasetF4_concatanated_tree.tre DatasetF4_DEAD_tree.tre DatasetF4_EF_tree.tre DatasetF4_IGS_tree.tre DatasetF4_ITS_tree.tre DatasetF4_RPB2_tree.tre # 4. The fasta files used for Recombination tests (for each dataset) -------------------------------------------------------------------- Recombination_DatasetF1.fas Recombination_DatasetF2.fas Recombination_DatasetF3_concatanated.fas Recombination_DatasetF3_DEAD.fas Recombination_DatasetF3_EF.fas Recombination_DatasetF3_ITS.fas Recombination_DatasetF4_BTUB.fas Recombination_DatasetF4_concatanated.fas Recombination_DatasetF4_DEAD.fas Recombination_DatasetF4_EF.fas Recombination_DatasetF4_IGS.fas Recombination_DatasetF4_ITS.fas Recombination_DatasetF4_RPB2.fas