Replication Data for: 'Gene gain, duplication and loss across the Metazoa Tree of Life'

Supplementary materials for the manuscript entitled 'Gene gain, duplication and loss across the Metazoa Tree of Life' by Rosa Fernández and Toni Gabaldón, published in Nature Ecology and Evolution. Documents included in this repository: Suppl. Mat. S1: Taxa included in this study. Accession numbers are indicated. Suppl. Mat. S2: Gene gain/loss values under the 'Porifera first' hypothesis. Suppl. Mat. S3: Raw values of gene gain/loss/duplication ratios for each dataset. Suppl. Mat. S4: Orthology tables for each dataset. Suppl. Mat. S5: Orthogroups inferred with OrthoFinder for each dataset. Number of duplications per taxon is indicated. Suppl. Mat. S6: GO enrichment analyses (fatiGO output files). If no enrichment was detected, no files were uploaded. Suppl. Mat. S7: eggNOG-mapper annotations of each genome and transcriptome, as well as the top 10 most duplicated orthogroups. Suppl. Mat. S8: Gene gain, duplication and loss values for each quartile of four selected phylomes to further test the effect of evolutionary rate and sequence length. Suppl. Mat. S9: Orthogroups in the metazoan gene repertoire. KEGG pathway annotation and total number of duplicates for each orthogroup are indicated. SpeciesTree_dataset2_rooted.nwk: Rooted species tree for dataset 2 (see Methods). SpeciesTree_dataset3_rooted.nwk: Rooted species tree for dataset 3 (see Methods).