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Erratum to: LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites
BMC Evolutionary Biology volume 9, Article number: 200 (2009)
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
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): 317-10.1186/1471-2148-8-317.
Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003, 19 (12): 1572-1574. 10.1093/bioinformatics/btg180.
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The online version of the original article can be found at 10.1186/1471-2148-8-317
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Grievink, L.S., Penny, D., Hendy, M.D. et al. Erratum to: LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evol Biol 9, 200 (2009). https://doi.org/10.1186/1471-2148-9-200
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DOI: https://doi.org/10.1186/1471-2148-9-200