Untrimmed and trimmed alignments (and selected alignments depicting N-terminal extensions) and phylogenetic trees in nexus and pdf format for plastid-associated and other proteins in eleftherids, Ichthyodinida and psammosids.

The dataset contains alignments (untrimmed and trimmed) and the corresponding phylogenetic trees (in nexus and pdf format) for plastid metabolic pathways (isoprenoid and FeS cluster biosynthesis; heme biosynthesis) and the lysine biosynthesis pathway enzyme DapL in eleftherids, Ichthyodinida and psammosids. For proteins with N-terminal extensions in eleftherids and/or Ichthyodinida, manually curated alignments to showcase putative plastid-targeting sequences are included. For selected heme proteins, curated alignments for the plastidial and cytosolic clades are included. The file names include the name of the protein and, in case of alignment (*.fasta) files, it is indicated whether the alignment is untrimmed or trimmed; for the tree files (*.tre and *.tre.pdf) the file name contains the protein name and the name of the model used for tree reconstruction.The untrimmed alignments have been filtered using PREQUAL with default options, before being aligned with MAFFT G-INS-i using the VSM option (--unalignlevel 0.6). The alignments were then subjected to Divvier using the -mincol 4 and the -divvygap option before trimming with trimAl (-gt 0.01). Trees were calculated with IQ-TREE, using the -mset option to restrict model selection to LG for ModelFinder, while branch support was assessed with 1000 ultrafast bootstrap replicates.