Bioinformatics is the computer-based analysis of the information content of biological molecules. This includes the amino acid sequences of proteins and the nucleotide sequences of nucleic acids such as RNA and DNA. Bioinformatics has many applications for the study of molecular biology and medicine. Its particular application to evolutionary science is that it allows the comparison of amino acid sequences in the corresponding proteins of different species, or the nucleotide sequences in the corresponding genes or noncoding DNA of different species.

Determining the nucleotide sequence of a DNA molecule used to be a lengthy and expensive process. The process developed by molecular biologist Frederick Sanger considerably shortened the work, which has now been entirely automated. The process uses nucleotides that cause DNA replication to stop, and that also have components that produce different colors of fluorescent light. When DNA fragments from this process are separated out according to size, they form a series of colored bands that look like a supermarket bar code. The sequence of red, green, blue, and yellow bands directly represents the sequence of the four nucleotides in the original DNA molecule. Thousands of DNA sequences have now been determined in laboratories all around the world. Whenever scientists publish papers that include reference to these sequences, the journal requires that the sequence be submitted to an electronic database that is accessible to scientists (or to anyone else) throughout the world. Two major databases are at the National Center for Biotechnology Information (NCBI), sponsored by the U.S. National Institutes of Health, and the Expert Protein Analysis System (ExPASy) in Switzerland. NCBI has databased DNA from more than 165,000 organisms.

Comparing nucleotide sequences also used to be a lengthy process, in which the nucleotides of each DNA molecule were compared to the corresponding nucleotides of another, one by one. Automated programs now line up the DNA molecules, identify the nucleotides that differ among the molecules, and calculate the percent similarities among them. Perhaps the most commonly used system is the Basic Local Alignment Search Tool (BLAST), also available at the NCBI web site. The single-nucleotide differences among DNA molecules, known as single nucleotide polymorphisms (SNPs), are often used as the data in the construction of phylogenetic trees . . .

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