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Bioinformatics Advance Access published online on October 22, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp600
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Ancestors 1.0: A Web Server For Ancestral Sequence Reconstruction

Abdoulaye Banire Diallo 1,2,*, Vladimir Makarenkov 1 and Mathieu Blanchette 2

1 Departement of computer science,Université du Québec à Montréal, PO.Box 8888 downtown station, Montreal Qc, H3C 3P8, Canada.
2 School of Computer Science, McGill University, 3630 University street #3107, Montreal, Qc, H3A2B2, Canada

*To whom correspondence should be addressed. Dr. Abdoulaye Baniré Diallo, E-mail: diallo.abdoulaye{at}uqam.ca


  Abstract

Summary: The computational inference of ancestral genomes consists of five difficult steps: Identifying syntenic regions, inferring ancestral arrangement of syntenic regions, aligning multiple sequences, reconstructing the insertion and deletion history, and finally inferring substitutions. Each of these steps have received lot of attention the past years. However, there currently exists no framework that integrates all of the the different steps in an easy workflow. Here, we introduce Ancestors 1.0, a web server allowing one to easily and quickly perform the last three steps of the ancestral genome reconstruction procedure. It implements several alignment algorithms, an indel maximum likelihood solver and a contextdependent maximum likelihood substitution inference algorithm. The results presented by the server include the posterior probabilities for the last two steps of the ancestral genome reconstruction and the expected error rate of each ancestral base prediction.

Availability: The Ancestors 1.0 is available at <http://ancestors.bioinfo.uqam.ca/ancestorWeb/>.

Contact: diallo.abdoulaye{at}uqam.ca

Associate Editor: Prof. Martin Bishop

Received on August 17, 2009; revised on September 15, 2009; accepted on October 2, 2009

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