REVIEW DATA PACKAGE FROM MORALES-BRIONES ET AL (SYSTEMATIC BIOLOGY USYB-2021-038.R1) Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae) This package contains the supplemental figures and tables referenced in the main text - Supplemental_material.zip It also contains the data and software outputs (i.e. fasta filtes, alignments, trees, logs, etc) - Analyses_data.tar.gz Supplemental_material.zip Supplemental figures S1-S12 Supplemental tables S1-S6 Analyses_data.tar.gz 1_original_fasta_files: Unaligned fasta files (*.fa) 2_raw_homologs: raw homolog trees. Cleaned alignments with Phyx (*.aln-cln) and RAxML bipartition labeled trees (*.tre) 3_final_homologs: filtered homologs (monophyletic clades and paraphyletic grades of same species masked, spurious tips removed with TreeShrink) 4_orthologs 1_MO (monophyletic outgroups): 1_fasta_to_trees: fasta files, alignments, ortholog trees 2_analyses: ASTRAL, WGD mapping, Phyparts, QuartetSampling, RAxML 2_RT (rooted ingroups): 1_fasta_to_trees: fasta files, alignments, ortholog trees 2_analyses: ASTRAL, WGD mapping, Phyparts, QuartetSampling, RAxML 5_analyses_with_homologs 1_ASTRAL-pro: : multilabeled homologs tres, ASTRAL-pro, Phyparts 2_grampa: GRAMPA analyses with complete and reduced trees 3_Phyparts_Informative_trees: MO and RT with all homologs and only with longest homologs 6_cpDNA: fasta files, alignment, QuartetSampling 7_Ks_plots: CDS and PEP files, Ks values (within-species and between-species) 8_other_files: HybPiper references, gene list, list of longest exons, gene annotations, If you have any question, please do not hesitate to contact me dfmoralesb@gmail.com Diego F. Morales-Briones