New Option for Pixel
The Pixel tool provides quality control for alignments by color coding each residue in a graphical image. Two new color schemes allow the user to color the residues relative to the first sequence in the alignment, thus making some misalignments easier to see. 27 April 2012

Search Interface Amino Acid Options
The HIV Sequence Database now stores amino acid translations. The Search Interface now allows searches for amino acid motifs, and users can download aligned amino acid sequences in the correct reading frame. 26 April 2012

2011 Web Gene Alignments
The Web Gene Alignments are available online. 29 March 2012

New Features for Epitope Location Finder (ELF)
ELF displays known and predicted epitopes found within a protein sequence query. ELF results now include both Class I (CTL) and Class II (helper) epitopes. In addition to predicting epitopes based on anchor residues, ELF now includes predictions from the Class I and Class II Binding Predictions tools at the Immune Epitope Database (IEDB). 13 March 2012

New Features for HIV BLAST
HIV BLAST has new features. It now allows the user to find best matches among only subtyped sequences, or sequences of a specific subtype. It allows the resulting sequences to be downloaded fully aligned. 01 March 2012

New Option for N-GlycoSite
The N-GlycoSite tool predicts N-linked glycosylation sites in amino acid sequences. A new option allows the user to exclude sites with a second-position proline, which is disfavored for N-linked glycosylation. 29 February 2012