Table 1.

Selected Bio.SeqIO or Bio.AlignIO file formats

Format	R/W	Name and reference
fasta	R+W	FASTA (Pearson and Lipman, 1988)
genbank	R+W	GenBank (Benson et al., 2007)
embl	R	EMBL (Kulikova et al., 2006)
swiss	R	Swiss-Prot/TrEMBL or UniProtKB
		(The UniProt Consortium, 2007)
clustal	R+W	Clustal W (Thompson et al., 1994)
phylip	R+W	PHYLIP (Felsenstein, 1989)
stockholm	R+W	Stockholm or Pfam (Bateman et al., 2004)
nexus	R+W	NEXUS (Maddison et al., 1997)

Where possible, our format names (column ‘Format’) match BioPerl and EMBOSS (Rice et al., 2000). Column ‘R/W’ denotes support for reading (R) and writing (W).