ABSTRACT
Homology is the cornerstone of phylogenomics and can be established at two levels for genes. The first level of homology is the level of genes in genomes, where the goal is to determine which genes or genomic regions are homologous. The second level of homology is the level of sequences in genes, where the goal is to determine which residue positions in genes, proteins, and noncoding regions are homologous (orthologous). BLAST is a widely used tool to identify matches that are inexact but have high similarity. It is optimized for searching a query sequence of nucleotides or amino acids against a large database of sequences, such as the nucleotide database on GenBank. Whole genomes can also be aligned to each other.
