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Bioinformatics Advance Access published online on July 14, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl387
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received May 1, 2006
Revised July 5, 2006
Accepted July 6, 2006

Applications note

Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network

Patricia Buendia 1 and Giri Narasimhan 1 *

1 Bioinformatics Research Group (BioRG), School of Computing and Information Science, Florida International University, Miami, FL 33199, USA

* To whom correspondence should be addressed.
Giri Narasimhan, E-mail: giri{at}cis.fiu.edu


  Abstract

Summary: Serial NetEvolve is a flexible simulation program that generates DNA sequences evolved along a tree or recombinant network. It offers a user-friendly Windows graphical interface and a Windows or Linux simulator with a diverse selection of parameters to control the evolutionary model. Serial NetEvolve is a modification of the Treevolve program with the following additional features: simulation of serially-sampled data, the choice of either a clock-like or a variable rate model of sequence evolution, sampling from the internal nodes and the output of the randomly generated tree or network in our newly proposed NeTwick format.

Availability: From website [http://biorg.cis.fiu.edu/SNE].

Supplementary information: Manual and examples available from: http://biorg.cis.fiu.edu/SNE.

Associate Editor: Keith A Crandall
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[Abstract] [Full Text] [PDF]


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