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Protein and Associated NucleotideDomains with Inferred Trees

PANDIT information page

PANDIT is a collection of multiple sequence alignments and phylogenetic trees. It contains corresponding amino acid and nucleotide sequence alignments, with trees inferred from each alignment. PANDIT is based on the Pfam database (Protein families database of alignments and HMMs), and includes the seed amino acid alignments of most families in the Pfam-A database. DNA sequences for as many members of each family as possible are extracted from the EMBL Nucleotide Sequence Database and aligned according to the amino acid alignment. PANDIT also contains a further copy of the amino acid alignments, restricted to the sequences for which DNA sequences were found.

For each alignment in the PANDIT database, a phylogenetic tree has been inferred using automated, but reasonably advanced, methods (see reference below for details, and Release notes for information on updates since then). Trees are available for download, and can be viewed graphically online.

The PANDIT can imagine many uses for this database, but we are particularly optimistic that it will help in the devising of improved mathematical models of amino acid and codon sequence evolution and for investigation of the effects of selection on protein sequence evolution.

Email notification of PANDIT news
If you would like to receive e-mail notification of new releases and significant updates to Pandit, please e-mail us at pandit@ebi.ac.uk.

Further detailed information for PANDIT

To cite PANDIT, please mention the paper above and our home page: http://www.ebi.ac.uk/research/goldman/software/pandit.

Phylogenetic trees are viewed using a modified version of Christian Zmasek's ATV
Pandit web site designed by Emmanuel Quevillon; thanks also to Nicolas Rodriguez.