Supplementary data for: Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates

Supplementary data for phylogenomic analysis in "Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates" by Nakayama, T., Nomura, M., Yabuki, A., Shiba, K., Inaba, K., & Inagaki, Y. (https://www.nature.com/articles/s41598-024-63502-0; https://doi.org/10.1101/2024.01.11.574452).

The text file CregCyn_phylogenomic_tree.newick contains a newick formatted phylogenomic tree shown in Figure 2 of the paper. Note that the tree is unrooted.
The compressed file phylogenomic_analysis_dataset.tar.gz contains the following directories and files.

• concatenated_dataset.fasta : dataset used for the phylogenomic analysis, constructed by combining 143 protein alignments.
• single_protein_datasets: directory containing each orthologous protein sequence from which the concatenated dataset was derived.
  It also contains the following subdirectories.
  • original_sequences: contains the multi-FASTA files of the original sequences for each orthologous protein.
  • multiple_alignments: contains multiple alignments for each orthologous protein.
  • trimmed_alignments: contains multiple alignments for each protein, with positions not suitable for analysis removed. These files are combined into single_protein_dataset.fasta.