Abstract
In this paper we present the ADOPS (Automatic Detection Of Positively Selected Sites) software that is ideal for research projects involving the analysis of tens of genes. ADOPS is a novel software pipeline that is being implemented with the goal of providing an automatic and flexible tool for detecting positively selected sites given a set of unaligned nucleotide sequence data.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Fu, Y.X.: Statistical Tests of Neutrality of Mutations Against Population Growth, Hitchhiking and Background Selection. Genetics 147(2), 915–925 (1997)
Hudson, R.R., Kreitman, M., Aguade, M.: A Test of Neutral Molecular Evolution Based on Nucleotide Data. Genetics 116(1), 153–159 (1987)
Tajima, F.: Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism. Genetics 123(3), 585–595 (1989)
Yang, Z., Nielsen, R.: Synonymous and nonsynonymous rate variation in nuclear genes of mammals. Journal of Molecular Evolution 46, 409–418 (1998)
Pond, S.L.K., Frost, S.D.W., Muse, S.V.: HyPhy: hypothesis testing using phylogenies. Bioinformatics 21(5), 676–679 (2005)
Guirao-Rico, S., Aguad, M.: Molecular evolution of the ligands of the insulin-signaling pathway: dilp genes in the genus Drosophila. Mol. Biol. Evol. 28(5), 1557–1560 (2011)
Reis, M., Sousa-Guimares, S., Vieira, C., Sunkel, C., Vieira, J.: Drosophila genes that affect meiosis duration are among the meiosis related genes that are more often found duplicated. Plos One 10(3), e17512 (2011)
Notredame, C., Higgins, D.G., Heringa, J.: T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302(1), 205–217 (2000)
Huelsenbeck, J.P., Ronquist, F.: MRBAYES: bayesian inference of phylogenetic trees. Bioinformatics 17(8), 754–755 (2001)
Yang, Z.: PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular Biology and Evolution 24 (2007)
Glez-Peña, D., Gómez-López, G., Reboiro-Jato, M., Fdez-Riverola, F., Pisano, D.G.: PileLine: a toolbox to handle genome position information in next-generation sequencing studies. BMC Bioinformatics 12(1) (2011)
Glez-Peña, D., Reboiro-Jato, M., Maia, P., Rocha, M., Díaz, F., Fdez-Riverola, F.: AIBench: A rapid application development framework for translational research in biomedicine. Computer Methods and Programs in Biomedicine 98, 191–203 (2010)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Reboiro-Jato, D., Reboiro-Jato, M., Fdez-Riverola, F., Fonseca, N.A., Vieira, J. (2012). On the Development of a Pipeline for the Automatic Detection of Positively Selected Sites. In: Rocha, M., Luscombe, N., Fdez-Riverola, F., Rodríguez, J. (eds) 6th International Conference on Practical Applications of Computational Biology & Bioinformatics. Advances in Intelligent and Soft Computing, vol 154. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28839-5_26
Download citation
DOI: https://doi.org/10.1007/978-3-642-28839-5_26
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-28838-8
Online ISBN: 978-3-642-28839-5
eBook Packages: EngineeringEngineering (R0)