HIV Molecular Immunology Database

TreeRate
We have released TreeRate, a web tool for re-rooting trees. Trees can be re-rooted using several methods including algorithms that optimize roots using single or multiple longitudinal samples. The intention of re-rooting the trees is to find the most homogeneous ("clocklike") evolutionary rate in the tree. Our previous tool Branchlength is now part of the TreeRate tool. 11 March 2009

RSS Feeds
The HIV Databases now offer the option to subscribe to RSS feeds. These RSS feeds will consist of all updates that appear in our News. 11 March 2009

Special Interest Alignments
A new page provides HIV sequence alignments and accompanying data of special interest to research. Each set of data consists of one or more DNA sequence alignments, references, and any accompanying data that are available. Sets are selected for inclusion based on availability and the likelihood that researchers will have an interest in using the data in other studies. Your help is needed to suggest or provide additional sets of data for inclusion. 11 March 2009

PepMap
New tool PepMap is available. The tool maps an input set of peptides on the HXB2 reference sequence, generates a table with peptide locations and peptide protein maps, similar to epitope maps. 23 February 2009

We have created a new Intra-patient Sequence Search interface (IPsearch). This interface is designed especially for retrieving longitudinal or other large intra-patient sequence sets. The interface is entirely functional, but will probably undergo small modifications over the coming weeks to optimize it. The link to it is in the 'Search' menu. 20 January 2009

We now provide an interface to PhyML, which generates much better trees than our simple Treemaker tool. The ML method is resource intensive, please try not to overload it. 16 January 2009

We migrated the HIV sequence database from Sybase to PostgreSQL. In the process we updated the Sequence Search Interface, the Advanced Search, the Geography Search Interface, and some minor tools associated with the database. 13 January 2009