Searching NCBI for Phylogenetic Data :: Phylogenetic Analysis (Bioinformatics Toolbox)

Bioinformatics Toolbox

Searching NCBI for Phylogenetic Data

The NCBI taxonomy Web site includes phylogenetic and taxonomic information from many sources. These sources include the published literature, Web databases, and taxonomy experts. And while the NCBI taxonomy database is not a phylogenetic or taxonomic authority, it can be useful as a gateway to the NCBI biological sequence databases.

This procedure uses the family Hominidae (orangutans, chimpanzees, gorillas, and humans) as a taxonomy example for searching the NCBI Web site and locating mitochondrial D-loop sequences.

Use the MATLAB Help browser to search for data on the Web. In the MATLAB Command Window, type
```
web('http://www.ncbi.nlm.nih.gov')
```
A separate browser window opens with the home page for the NCBI Web site.
Search the NCBI Web site for information. For example, to search for the human taxonomy, from the Search list, select Taxonomy, and in the for box, enter hominidae.

The NCBI Web search returns a list of links to relevant pages.
Select the taxonomy link for the family Hominidae. A page with the taxonomy for the family is shown.

Overview for the Primate Example

Creating a Phylogenetic Tree for Five Species