7.2. Obtaining and formatting sequences of interest for phylogenetics

Once you have obtained DNA sequence data for your study, you may wish to add accessioned sequence data to your analyses. This will be particularly important if you want to root your phylogeny and provide an outgroup (sequence(s) to which all of your sequences are distantly related) to strengthen comparative interpretation of your data. Accessions from nucleotide sequence data banks can be searched, using a keyword(s) or via a BLAST search algorithm (i.e. blastn, megablast, etc.), to identify homologues to your sequence of interest. These include GenBank (via NCBI; (http://www.ncbi.nlm.nih.gov/), EMBL-Bank (via EBI; http://www.ebi.ac.uk/embl/), and DNA Data Bank of Japan (DDBJ; http://ddbj.sakura.ne.jp/).  If using rRNA sequence data, SILVA rRNA database (http://www.arb-silva.de/) can be used to retrieve reference sequences that are quality-scored (Pruesse et al., 2007).