The Phaeoexplorer project sequenced 60 genomes corresponding to 44 brown algal and sister species. This dataset corresponds to supplementary information relating to the initial annotation of the Phaeoexplorer genomes and multiple analyses of the genome data. The dataset includes presubmission (v0) versions of the Phaeoexplorer genome annotation (GFF) files (GFF_v0.tar.gz) and genome-wide predicted proteomes as fasta files (Proteomes_v0.tar.gz), de novo transcriptome assemblies for the Phaeoexplorer species (RNA-seq data assembled with Trinity or rnaSPAdes; de-novo-transcriptomes.tar.gz), RepeatMasker analyses of repeat sequences (RepeatMasker.tar.gz), alignment files used to generate a phylogenetic tree for the Phaeoexplorer species (PhylogeneticTree.tar.gz), alignments used to build a densitree specifically for Ectocarpus species (Microevolution_Ectocarpus.tar.gz), an Orthofinder-based analysis of shared orthologues (Orthogroups.tar.gz) together with a Dollo-logic-based analysis of orthogroup gain and loss during evolution (Dollo_analysis.tar.gz), a Phylostratigraphy analysis of brown algal genes (Phylostratigraphy.tar.gz), an analysis of protein functional domain fissions and fusions (CompositeGenes.tar.gz), Interproscan analyses of protein domains (InterProScan.tar.gz), Hectar predictions of protein subcellular localisations (Hectar.tar.gz), eggNOG output providing information about predicted protein functions (eggNOG.tar.gz), RNA-seq-based data on gene expression levels (mRNAexpression.tar.gz), results of a search for genes acquired via horizontal gene transfer (HGT.tar.gz), analyses of intron conservation across genomes (Introns_conservation.tar.gz), an analysis of tandem gene duplications (Tandemely_duplicated_genes.tar.gz), comparisons of CDS size with the Ectocarpus reference genome that were used to evaluate gene model completeness (CDS_size.tar.gz), a DESeq2 analysis of differential gene expression between the sporophyte and gametophyte generations of several brown algal species (DEG_LifeCycle.tar.gz), information about orthogroups selected to analyse the effects of morphological complexity and life cycle structure on gene evolution (Genes_selection.tar.gz). Each individual dataset contains a README file explaining its content. Detailed information about the methodology used for each analysis can be found in the Methods section of the manuscript preprint (https://doi.org/10.1101/2024.02.19.579948). The majority of these analyses and datasets can also be accessed via the Phaeoexplorer website (https://phaeoexplorer.sb-roscoff.fr/).