Assembled transcriptomes, individual gene alignments, concatenated and trimmed alignments, tree files for the phylogenomic dataset including eleftherids, Ichthyodinida and psammosids.

The dataset contains the concatenated and trimmed alignment and corresponding Maximum-likelihood (ML) multi-protein tree for phylogenomic analysis of eleftherids, Ichthyodinida (MALV-I) and psammosids. Transcriptomes assembled from raw reads are provided in the "transcriptomes" folder. The individual proteins concatenated for phylogenomic analysis are in the "individual_proteins" folder. Individual proteins and the corresponding phylogenomic files with additional SAG data from Delmont <i>et al.</i> 2022 are included in "wDelmont2022SAGs" Transcriptomes were assembled with Trinity (eleftherids) or rnaSPAdes (Ichthyodinida, psammosids) and protein coding regions were predicted using TransDecoder. Homologues to the 263 genes described in Burki <i>et al. </i>2016 were identified using BLAST, aligned with MAFFT L-ins-i and trimmed with trimAL (gap threshold of 80%). Single-protein ML phylogenies were reconstructed and manually cleaned to remove paralogues/contamination. Cleaned proteins were then aligned and trimmed as above and concatenated with SCaFOs. ML trees of the final concatenated alignment were generated with IQ-TREE using the LG+C60+F+G4 model.