Skip Navigation


Nucleic Acids Research Advance Access originally published online on May 13, 2009
Nucleic Acids Research 2009 37(Web Server issue):W179-W184; doi:10.1093/nar/gkp370
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (3758K) Freely available
Right arrow Screen PDF (481K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
37/suppl_2/W179    most recent
gkp370v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Bruggeman, J.
Right arrow Articles by Brandt, B. W.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bruggeman, J.
Right arrow Articles by Brandt, B. W.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W179-W184
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

PhyloPars: estimation of missing parameter values using phylogeny

Jorn Bruggeman1,*, Jaap Heringa2 and Bernd W. Brandt2

1Department of Theoretical Biology, Faculty of Earth & Life Sciences and 2Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, The Netherlands

*To whom correspondence should be addressed. Tel: +31 20 5986959; Fax: +31 20 5987123; Email: jorn.bruggeman{at}falw.vu.nl

Received February 6, 2009. Revised April 22, 2009. Accepted April 24, 2009.

A wealth of information on metabolic parameters of a species can be inferred from observations on species that are phylogenetically related. Phylogeny-based information can complement direct empirical evidence, and is particularly valuable if experiments on the species of interest are not feasible. The PhyloPars web server provides a statistically consistent method that combines an incomplete set of empirical observations with the species phylogeny to produce a complete set of parameter estimates for all species. It builds upon a state-of-the-art evolutionary model, extended with the ability to handle missing data. The resulting approach makes optimal use of all available information to produce estimates that can be an order of magnitude more accurate than ad-hoc alternatives. Uploading a phylogeny and incomplete feature matrix suffices to obtain estimates of all missing values, along with a measure of certainty. Real-time cross-validation provides further insight in the accuracy and bias expected for estimated values. The server allows for easy, efficient estimation of metabolic parameters, which can benefit a wide range of fields including systems biology and ecology. PhyloPars is available at: http://www.ibi.vu.nl/programs/phylopars/.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.