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bioRxiv · 10.1101/338442

Dimension Reduction and Visualization for Single-copy Alignments via Generalized PCA

Rohrlach, A. B.·Bean, N.·Glonek, G.·Holland, B.·Tobler, R.·Tuke, J.·Cooper, A.
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Abstract

Single-copy sequence alignments have been a valuable source of information for genetic studies; their lack of recombination makes phylogenetic analyses tractable [1]. Specifically, mitochondrial DNA will continue to play an important role in genetic studies due to its high mutation rate and high copy per cell count of the molecule [2]. In this paper we develop a new method for the analysis of single-copy sequence data that simultaneously considers the relationships between sequenced individuals and positions of interest in the genome. We then show that tests for relationships between genetic information and qualitative and quantitative characteristics can be calculated. We motivate the use of our method with examples from empirical data.

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Rohrlach, A. B., Bean, N., Glonek, G., Holland, B., Tobler, R., Tuke, J., Cooper, A.. 2018-06-04. Dimension Reduction and Visualization for Single-copy Alignments via Generalized PCA. https://doi.org/10.1101/338442

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