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Bioinformatics Advance Access published online on December 20, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl634
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 7, 2006
Accepted December 11, 2006

Applications note

URec: a system for unrooted reconciliation

Pawel Górecki 1 *

1 Warsaw University, Institute of Informatics, Banacha 2, 02-678 Warsaw, Poland; Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany

* To whom correspondence should be addressed.
Pawel Górecki, E-mail: gorecki{at}mimuw.edu.pl


  Abstract

Summary: URec is a software based on a concept of unrooted reconciliation. It can be used to reconcile a set of unrooted gene trees with a rooted species tree or a set of rooted species trees. Moreover, it computes detailed distribution of gene duplications and gene losses in a species tree. It can be used to infer optimal species phylogenies for a given set of gene trees. URec is implemented in C++ and can be easily compiled under Unix and Windows systems.

Availability: Software is freely available for download from our website at http://bioputer.mimuw.edu.pl/_gorecki/urec. This webpage also contains Windows executables and a number of advanced examples with explanations.

Associate Editor: Joaquin Dopazo
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