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Nucleic Acids Research 2006 34(Database Issue):D327-D331; doi:10.1093/nar/gkj087
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Nucleic Acids Research, 2006, Vol. 34, Database issue D327-D331
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees

Simon Whelan*, Paul I. W. de Bakker1, Emmanuel Quevillon, Nicolas Rodriguez and Nick Goldman

EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK 1Department of Molecular Biology, Massachussetts General Hospital Boston, MA 02114, USA

*To whom correspondence should be addressed. Tel: +44 1223 494655; Fax: +44 1223 494468; Email: simon{at}ebi.ac.uk

Received September 15, 2005. Revised October 12, 2005. Accepted October 12, 2005.

PANDIT is a database of homologous sequence alignments accompanied by estimates of their corresponding phylogenetic trees. It provides a valuable resource to those studying phylogenetic methodology and the evolution of coding-DNA and protein sequences. Currently in version 17.0, PANDIT comprises 7738 families of homologous protein domains; for each family, DNA and corresponding amino acid sequence multiple alignments are available together with high quality phylogenetic tree estimates. Recent improvements include expanded methods for phylogenetic tree inference, assessment of alignment quality and a redesigned web interface, available at the URL http://www.ebi.ac.uk/goldman-srv/pandit.

Present address: Emmanuel Quevillon, URGI-INRA, 523 Place des Terrasses, 91000, Evry, France


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