Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts".

<p>Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts". The data set consists of five folders: &ldquo;Codon_usage_amoebae_and_viruses&rdquo;, "Genome_annotations_amoebae", "Phylogenetic_trees_18S_amoebae", &ldquo;Phylogenomic_trees_amoebae&rdquo;, and "Viral_integration_detection_amoebae". The &ldquo;Codon_usage_amoebae_and_viruses&rdquo; folder contains for each amoeba host the calculated codon usage tables in the subfolder "codon_usage_table_host", the calculated codon usage preferences using different scores in the subfolder "codon_usage_scores_host", and the calculated codon usage preferences of giant viruses versus each host in the subfolder "codon_usage_scores_viruses_vs_host". The giant viruses in the subfolder "codon_usage_scores_viruses_vs_host" are organised by viral family and genus in separate sub-subfolders. The "Genome_annotations_amoebae" folder contains the generated genome annotations in different formats and the manually curated mitochondrial genome annotations for each amoeba host.&nbsp; The "Phylogenetic_trees_18S_amoebae" contains for the eukaryotic phyla <em>Discosea</em>, <em>Heterolobosea</em>, and <em>Tubulinea,&nbsp;</em>the 18S rRNA&nbsp;nucleotide alignments, distance matrices, and computed phylogenetic trees. The folder "Phylogenomic_trees_amoebae" contains for the eukaryotic clades <em>Amoebozoa</em> and <em>Discoba,&nbsp;</em>the protein alignment matrices and computed phylogenomic trees. The folder "Viral_integration_detection_amoebae" contains the MCP databases used (fasta file, alignment file, HMM profile and DIAMOND BLASTX database) and the MCP sequences detected in this study and the blast results of these.&nbsp;&nbsp;</p>