The zip files includes alignments of protein sequences in fasta format (SequenceAlignments.zip) and their concatenated sets used in our research project (ConcatenatedAlignments.zip). Additionally, we included raw (unaligned) protein sequences in fasta format (RawSequences.zip). In total, we employed 97 amino acid sequences of conserved plastid-encoded proteins, carefully selected from the NCBI reference sequence database (https://www.ncbi.nlm.nih.gov/refseq/), and GenBank (https://www.ncbi.nlm.nih.gov/genbank/), representing 112 organisms. Our dataset included 111 eukaryotes carrying red-alga derived plastids and the closest plastid cyanobacterial relative Gloeomargarita lithophora Alchichica D10. We performed independent alignments of each homologous protein group using a slow and accurate L-INS-i algorithm implemented in MAFFT v7.429 (https://doi.org/10.1093/molbev/mst010). The resulting multiple sequence alignments were carefully assessed using AliView (http://dx.doi.org/10.1093/bioinformatics/btu531), and phylogenetically informative sites were selected through trimAl https://doi.org/10.1093/bioinformatics/btp348and ClipKIT (https://doi.org/10.1371/journal.pbio.3001007). The trimmed alignments were concatenated into supermatrices using SequenceMatrix 1.8 (https://doi.org/10.1111/j.1096-0031.2010.00329.x)to generate comprehensive datasets for phylogenetic and molecular clock analyses. We also generated a supermatrix composed of untrimmed alignments.