Comparative mitogenomics reveals evolutionary drivers of Strongyloidea nematodes dwelling in gastrointestinal tract

This dataset includes mitochondrial protein-coding genes (PCGs) and ribosomal RNA genes (rrnL and rrnS) from 12 species, prepared for phylogenetic and evolutionary analyses through a standardized alignment and filtering pipeline.<b>Multiple Sequence Alignment</b><br>Protein sequences of mitochondrial PCGs and ribosomal RNAs were aligned using MAFFT with global alignment mode, which is suitable for homologous sequences. The output is a comprehensive multi-sequence alignment file (<code>alignment.fas</code>) containing both protein and rRNA data.<b>Protein-to-Nucleotide Alignment Conversion</b><br>To ensure codon-level accuracy in subsequent nucleotide analyses, PAL2NAL was used to convert the protein alignments back into nucleotide alignments. This step corrects potential frameshifts or misalignments due to sequencing errors and ensures that the codon structure is maintained. The result is a codon-aware nucleotide alignment (<code>nucleotide_alignment.fas</code>).<b>Conserved Region Filtering</b><br>Gblocks was employed to remove poorly aligned or highly variable regions from the nucleotide alignment. Parameters were set to default or adjusted to allow a moderate number of gaps, depending on alignment quality. The final output (<code>alignment_gblocks.fas</code>) consists of high-confidence conserved regions, suitable for downstream phylogenetic inference.This workflow ensures alignment accuracy at both the amino acid and nucleotide levels, providing high-quality input data for reliable evolutionary analyses.