# Spectral analysis of phylogenetic data

@article{Hendy1993SpectralAO, title={Spectral analysis of phylogenetic data}, author={Michael D. Hendy and David Penny}, journal={Journal of Classification}, year={1993}, volume={10}, pages={5-24} }

The spectral analysis of sequence and distance data is a new approach to phylogenetic analysis. For two-state character sequences, the character values at a given site split the set of taxa into two subsets, a bipartition of the taxa set. The vector which counts the relative numbers of each of these bipartitions over all sites is called a sequence spectrum. Applying a transformation called a Hadamard conjugation, the sequence spectrum is transformed to the conjugate spectrum. This conjugationâ€¦Â Expand

#### 195 Citations

Phylogenetic analysis based on spectral methods.

- Biology, Medicine
- Molecular biology and evolution
- 2012

Through simulations, it is shown that the covariance-based methods effectively capture phylogenetic signal even when structural information is not fully retained, and Comparisons of simulation results with the bootstrap permutation results indicate that the covariances are fairly robust under perturbation in sequence similarity but more sensitive to perturbations in structural similarity. Expand

The sampling distributions and covariance matrix of phylogenetic spectra

- Biology
- 1994

Recent advances in computing variance-covariance matrices from genetic distances to a sequence method of phylogenetic analysis are extended and the bias induced by the delta method, a convenient approximation in deriving V[y], is evaluated and found to be acceptable in the first case and very good in the second. Expand

Generalizing Phylogenetic Parsimony from the Tree to the Forest

- Biology
- 1998

This multitree approach is a simple generalization of cladistic parsimony to reticulate systems of common ancestry, which can be attributed to the algorithmic and conceptual simplicity of trees and the expecta- tion that certain evolutionary processes gener- ate treelike descent patterns. Expand

Distinguishing Convergence on Phylogenetic Networks

- Biology, Mathematics
- 2016

It is shown how methods from algebraic geometry, such as Grobner bases, can be used to solve the polynomial equations in phylogenetics and some four-taxon trees and networks can be distinguished from each other. Expand

Phylogenetic tree-building.

- Biology, Medicine
- International journal for parasitology
- 1996

Cladistic analysis is an approach to phylogeny reconstruction that groups taxa in such a way that those with historically more-recent ancestors form groups nested within groups of taxa withâ€¦ Expand

The Effects of Sequence Length, Tree Topology, and Number of Taxa on the Performance of Phylogenetic Methods

- Mathematics, Computer Science
- J. Comput. Biol.
- 1994

Simulations were used to study the performance of several character-based and distance-based phylogenetic methods in obtaining the correct tree from pseudo-randomly generated input data, and it is shown that when the number of taxa, the maximum path length, and the minimum edge length are held constant, there it little but significant dependence of the performance on the tree topology. Expand

Application of Phylogenetic Network

- Biology
- 2012

The phylogenetic network revealed the following pattern: a recombinant allele had a short external branch and was located on a diagonal with the outgroup allele and the two parental alleles were located on another diagonal with long external branches. Expand

Building trees, hunting for trees, and comparing trees : theory and methods in phylogenetic analysis

- Mathematics
- 1997

Phylogenetics is the study and identification of evolutionary patterns and structures in nature; this thesis explores the mathematics of these structures. The basic objects of study are the leafâ€¦ Expand

Phylogenetic analyses of parasites in the new millennium.

- Biology, Medicine
- Advances in parasitology
- 2006

The review finishes with a detailed consideration of the analysis of a multi-gene data set for several dozen taxa of Cryptosporidium (Apicomplexa), illustrating many of the theoretical and practical points highlighted in the review. Expand

Measuring the fit of sequence data to phylogenetic model: allowing for missing data.

- Biology, Medicine
- Molecular biology and evolution
- 2005

It is fundamentally important to assess the fit of data to model in phylogenetic and evolutionary studies. Phylogenetic methods using molecular sequences typically start with a multiple alignment. Itâ€¦ Expand

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