Construction of molecular evolutionary phylogenetic trees from DNA sequences based on minimum complexity principle

Ren, Fengrong; Tanaka, Hiroshi; Gojobori, Takashi

doi:10.1016/0169-2607(94)01609-j

Cited by 3 publications

(2 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This would be a means to better understand what some biophysicists call the "complexity principle " in contemporary evolutionistic approaches. More 936 C. Riedberger AACA precisely, these daring ideas, which could have been derived from Clifford's, have recently been applied to the construction of molecular evolutionary phylogenetic trees (24). After Clifford, I believe that it would be interesting to see if any sort of "informational" kernel should prove to underlie the structure and dynamical behaviour of matter.…”

Section: A New Quantum Model Of the Mindmentioning

confidence: 99%

From Clifford’s Theory of Consciousness to A New Quantum Model of the Mind

Riedberger

2009

AACA

View full text Add to dashboard Cite

From the highly interesting and original Cliffordian concepts of "mind-stuff " and "eject ", I have derived some hypotheses about the possible new categories of the mind I have been working upon in ref.(1). Henceforth, drawing from Freud's own conception of the psychic apparatus, I give an account of what might constitute a new psychoanalytic and philosophical approach to Consciousness. More precisely, I propose new definitions of both the Conscious and the Unconscious systems and suggest there exists another agency that I have named the Exconscious system. In my new topography of the psychic apparatus, this new system corresponds to the superposition of the two other systems, unlike the Freudian Preconscious (which I have thus replaced). Interestingly, this new notion of superposition was already present in germs in Clifford's pioneering approach and is one of the leading hypotheses of Penrose's work.

show abstract

Section: A New Quantum Model Of the Mindmentioning

confidence: 99%

From Clifford’s Theory of Consciousness to A New Quantum Model of the Mind

Riedberger

2009

AACA

View full text Add to dashboard Cite

show abstract

“…The best hypothesis is the one that minimizes the length of the description of the hypothesis plus the length of the description of the data when encoded or compressed with the help of that hypothesis. Scientific inference based on some version of this idea has been applied to many biological problems, including sequence alignment (Allison et al, 1999(Allison et al, , 2000Allison and Yee, 1990), phylogeny reconstruction (Cheeseman and Kanefsky, 1993;Li et al, 2001;Milosavljevic et al, 1990;Otu and Sayood, 2003;Ren et al, 1995), and comparison of classifications (Day, 1983), though not to collections of trees constructed from separate data sets. In this framework, a hypothesis is either a tree or a collection of trees and the best hypothesis is the one that permits the maximum compression of that hypothesis plus the sequence alignment.…”

mentioning

confidence: 99%

Missing the Forest for the Trees: Phylogenetic Compression and Its Implications for Inferring Complex Evolutionary Histories

Ané

Sanderson

2005

Systematic Biology

View full text Add to dashboard Cite

Phylogenetic tree reconstruction is difficult in the presence of lateral gene transfer and other processes generating conflicting signals. We develop a new approach to this problem using ideas borrowed from algorithmic information theory. It selects the hypothesis that simultaneously minimizes the descriptive complexity of the tree(s) plus the data when encoded using those tree(s). In practice this is the hypothesis that can compress the data the most. We show not only that phylogenetic compression is an efficient method for encoding most phylogenetic data sets and is more efficient than compression schemes designed for single sequences, but also that it provides a clear information theoretic rule for determining when a collection of conflicting trees is a better explanation of the data than a single tree. By casting the parsimony problem in this more general framework, we also conclude that the so-called total-evidence tree--the tree constructed from all the data simultaneously--is not always the most economical explanation of the data.

show abstract

An Information-Theoretic Method for the Treatment of Plural Ancestry in Phylogenetics

Munshaw

Kepler

2008

Molecular Biology and Evolution

View full text Add to dashboard Cite

In the presence of recombination and gene conversion, a given genomic segment may inherit information from 2 distinct immediate ancestors. The importance of this type of molecular inheritance has become increasingly clear over the years, and the potential for erroneous inference when it is not accounted for in the statistical model is well documented. Yet, the inclusion of plural ancestry (PA) in phylogenetic analysis is still not routine. This omission is due to the greater difficulty of phylogenetic inference on general acyclic graphs compared that on with trees and the accompanying computational burden. We have developed a technique for phylogenetic inference in the presence of PA based on the principle of minimum description length, which assigns a cost--the description length--to each network topology given the observed sequence data. The description length combines the cost of poor data fit and model complexity in terms of information. This device allows us to search through network topologies to minimize the total description length. By comparing the best models obtained with and without PA, one can determine whether or not recombination has played an active role in the evolution of the genes under investigation, identify those genes that appear to be mosaic, and infer the phylogenetic network that best represents the history of the alignment. We show that the method performs well on simulated data and demonstrate its application on HIV env gene sequence data from 8 human subjects. The software implementation of the method is available upon request.

show abstract

Construction of molecular evolutionary phylogenetic trees from DNA sequences based on minimum complexity principle

Cited by 3 publications

References 16 publications

From Clifford’s Theory of Consciousness to A New Quantum Model of the Mind

From Clifford’s Theory of Consciousness to A New Quantum Model of the Mind

Missing the Forest for the Trees: Phylogenetic Compression and Its Implications for Inferring Complex Evolutionary Histories

An Information-Theoretic Method for the Treatment of Plural Ancestry in Phylogenetics

Contact Info

Product

Resources

About