Abstract
Phylotranscriptomics, the study of phylogenetic relationships among taxa based on their DNA sequences derived from transcriptomes, has recently emerged as the preferred method for studying evolutionary biology because of the relatively low cost of transcriptome sequencing compared with genome sequencing and the fact that phylotranscriptomics is almost as reliable as phylogenomics. However, it is challenging to perform transcriptomic and phylogenetic analyses together without programming expertise. In this study, we present a protocol for phylotranscriptomic analysis to aid molecular biologists unfamiliar with UNIX command-line interface and bioinformatics tools. We hope that our proposed protocol may serve as practical and useful information for the training and education of novice marine biologists.