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Open Access Correction

LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites

Liat Shavit Grievink*, David Penny, Mike D Hendy and Barbara R Holland

Author Affiliations

The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11 222, Palmerston North, New Zealand

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BMC Evolutionary Biology 2009, 9:200  doi:10.1186/1471-2148-9-200


The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2148/9/200


Received:12 August 2009
Accepted:13 August 2009
Published:13 August 2009

© 2009 Grievink et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Correction to Shavit Grievink L, Penny D, Hendy MD, Holland BR: LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evol Biol 2008, 8(1):317.

Correction

Since publication of our article [1], we discovered an error in the second example. For this example, we state in the paper, we used the program MrBayes [2] with the JC+I+Cov model. However, we now found that, albeit appearances, this model is not implemented in MrBayes [2]. In fact, no combination of I+Cov (e.g. HKY+I+Cov, GTR+G+I+Cov) is currently implemented in MrBayes [2]. Instead, the program ignores the I parameter, so tree reconstruction in this example was therefore effectively done using the JC+Cov model. This does not affect the conclusion of our paper that phylogenetic estimation can be misleading for sequence data simulated with lineage-specific properties.

References

  1. Shavit Grievink L, Penny D, Hendy MD, Holland BR: LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites.

    BMC Evol Biol 2008, 8(1):317. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  2. Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models.

    Bioinformatics 2003, 19(12):1572-1574. PubMed Abstract | Publisher Full Text OpenURL