As part of the CAFE Summer Scholars program, I had the opportunity to work with Mayrolin García Morales and Benjamin B. Normark on creating a phylogenetic tree using bioinformatics tools new to the lab. This project focused specifically on the genetics of scale insects, particularly armored scale insects (Diaspididae). During the project, we created SQLite3 and BLAST databases from raw read genomes and transcriptomes of scale insect Next-Generation Sequencing data. We then built assemblies from these databases and a multi-query bait sequence, through BLASTing the bait sequence against the BLAST databases for each taxon. This uncovered mate pairs for the BLAST hits in the SQLite3 database. Next, we utilized de novo assemblers to build contigs that would become the bait sequences for the next iteration. After that, we pieced together the assemblies using Exonerate. From there, the sequences were aligned with each taxon, and these alignments were concatenated for each locus. Finally, a phylogenetic tree with bootstrap support values and concordance factors was formed using the concatenated alignments. We hope that this process and the data collected will help further unravel the many cryptic species complexes found in scale insects.