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Evolutionary Bioinformatics

Synopsis: An open access, peer reviewed electronic journal that covers computational evolutionary biology and evolutionary bioinformatics.


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About this journal

Aims and scope:

Evolutionary Bioinformatics is an international, peer-reviewed journal focusing on evolutionary bioinformatics. There is growing awareness that to understand organismal form and function, through the use of molecular, genetic, genomic, and proteomic data, due consideration must be given to an organism's evolutionary context - history constrains the path an organism is obliged to take, and leaves an indelible mark on its component parts. Evolutionary Bioinformatics publishes papers on all aspects of computational evolutionary biology and evolutionary bioinformatics.

Editorial standards and procedures:

All submissions to this journal, with the exception of editorials and dedications (obituaries), are subject to rigorous peer review by a minimum of two peer reviewers who demonstrate current research experience in the paper's subject area.  Reviewers are required to provide in-depth, fair and objective reviews.  They may not act as reviewers if they are in a conflict of interest.  All final publishing decisions are made by the Editor in Chief or Associate Editor.

Official journal of the Bioinformatics Institute:

Evolutionary Bioinformatics was established as the official journal of The Bioinformatics Institute.  The Institute is a joint-venture between the University of Auckland, situated in New Zealand’s largest city, and AgResearch, New Zealand’s largest Crown Research Institute. Allen Rodrigo, Professor of Computational Biology and Bioinformatics, is the Institute’s Director, and it was at his initiative that the journal was established.

Working in collaboration with The Institute is Libertas Academica, a publishing firm committed to high editorial standards, open access publishing methodologies and superior user-service standards. There is much work involved ‘behind-the-scenes’ that goes towards the finished result seen by readers of Evolutionary Bioinformatics. Key amongst this work, which also includes attracting the best submissions, supervising effective peer review and typesetting, is gaining acceptance for indexing by outside organizations.

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This journal has been awarded a SPARC Europe Seal. The Seal is an initiative of SPARC Europe (Scholarly Publishing and Academic Resources Coalition) and the Directory of Open Access Journals (DOAJ) which is awarded to journals applying a Creative Commons CC-BY copyright license and that make journal metadata accessible to DOAJ.  

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As of April 7 2008, the US NIH Public Access Policy requires that all peer reviewed articles resulting from research carried out with NIH funding be deposited in the Pubmed Central archive.

If you are an NIH employee or grantee Libertas Academica will ensure that you comply with the policy by depositing your paper at Pubmed Central on your behalf. 

ISSN: 1176-9343


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Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations

Authors: Laurent Gatto, Daniele Catanzaro and Michel C. Milinkovitch
Publication Date: 04 Feb 2007
Evolutionary Bioinformatics 2006:2 145-155

Laurent Gatto, Daniele Catanzaro and Michel C. Milinkovitch

Laboratory of Evolutionary Genetics, Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, CP300, rue Jeener et Brachet 12, 6041 Gosselies, Belgium.

Abstract: The General Time Reversible (GTR) model of nucleotide substitution is at the core of many distance-based and character-based phylogeny inference methods. The procedure described by Waddell and Steel (1997), for estimating distances and instantaneous substitution rate matrices, R, under the GTR model, is known to be inapplicable under some conditions, ie, it leads to the inapplicability of the GTR model. Here, we simulate the evolution of DNA sequences along 12 trees characterized by different combinations of tree length, (non-)homogeneity of the substitution rate matrix R, and sequence length. We then evaluate both the frequency of the GTR model inapplicability for estimating distances and the accuracy of inferred alignments. Our results indicate that, inapplicability of the Waddel and Steel’s procedure can be considered a real practical issue, and illustrate that the probability of this inapplicability is a function of substitution rates and sequence length. We also discuss the implications of our results on the current implementations of maximum likelihood and Bayesian methods.



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