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1.
Peer Review #2 of "Fast and accurate estimation of the covariance between pairwise maximum likelihood distances (v0.1)"
Title:
Peer Review #2 of "Fast and accurate estimation of the covariance between pairwise maximum likelihood distances (v0.1)"
Author:
Steffen Klaere
Steffen Klaere
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Publisher:
PeerJ
Year of Publication:
2014
Document Type:
Text
Relations:
doi:10.7717/peerj.583
URL:
http://dx.doi.org/10.7287/PEERJ.583V0.1/REVIEWS/2
http://dx.doi.org/10.7287/PEERJ.583V0.1/REVIEWS/2
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2.
Preface
Open Access
Title:
Preface
Author:
Steffen Kläre
Steffen Kläre
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Description:
May they live long and prosper.
May they live long and prosper.
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Contributors:
The Pennsylvania State University CiteSeerX Archives
Year of Publication:
20080701
Source:
http://edoc.ub.unimuenchen.de/3992/1/
Klaere
_Steffen.pdf
http://edoc.ub.unimuenchen.de/3992/1/
Klaere
_Steffen.pdf
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Document Type:
text
Language:
en
Subjects:
Zusammenfassung
Zusammenfassung
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Rights:
Metadata may be used without restrictions as long as the oai identifier remains attached to it.
Metadata may be used without restrictions as long as the oai identifier remains attached to it.
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URL:
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.89.6471
http://edoc.ub.unimuenchen.de/3992/1/Klaere_Steffen.pdf
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.89.6471
http://edoc.ub.unimuenchen.de/3992/1/Klaere_Steffen.pdf
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3.
Phylogenetic diversity within seconds
Open Access
Title:
Phylogenetic diversity within seconds
Author:
Bui Quang Minh
;
Steffen Klaere
;
Arndt
;
Von Haeseler
Bui Quang Minh
;
Steffen Klaere
;
Arndt
;
Von Haeseler
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Description:
Abstract.—We consider a (phylogenetic) tree with n labeled leaves, the taxa, and a length for each branch in the tree. For any subset of k taxa, the phylogenetic diversity is defined as the sum of the branchlengths of the minimal subtree connecting the taxa in the subset. We introduce two timeefficient algorithms (greedy and pruning) to comput...
Abstract.—We consider a (phylogenetic) tree with n labeled leaves, the taxa, and a length for each branch in the tree. For any subset of k taxa, the phylogenetic diversity is defined as the sum of the branchlengths of the minimal subtree connecting the taxa in the subset. We introduce two timeefficient algorithms (greedy and pruning) to compute a subset of size k with maximal phylogenetic diversity in O(«log/c) and O[n + (n k) login k)] time, respectively. The greedy algorithm is an efficient implementation of the socalled greedy strategy (Steel, 2005; Pardi and Goldman, 2005), whereas the pruning algorithm provides an alternative description of the same problem. Both algorithms compute within seconds a subtree with maximal phylogenetic diversity for trees with 100,000 taxa or more. [Biodiversity conservation; Comparative genomics; Greedy algorithm; Phylogenetic diversity; Phylogenetic tree; Pruning algorithm.]
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Contributors:
The Pennsylvania State University CiteSeerX Archives
Year of Publication:
20130818
Source:
http://sysbio.oxfordjournals.org/content/55/5/769.full.pdf
http://sysbio.oxfordjournals.org/content/55/5/769.full.pdf
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Document Type:
text
Language:
en
Subjects:
Recently ; Steel (2005) and Pardi and Goldman (2005
Recently ; Steel (2005) and Pardi and Goldman (2005
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Rights:
Metadata may be used without restrictions as long as the oai identifier remains attached to it.
Metadata may be used without restrictions as long as the oai identifier remains attached to it.
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URL:
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.330.5079
http://sysbio.oxfordjournals.org/content/55/5/769.full.pdf
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.330.5079
http://sysbio.oxfordjournals.org/content/55/5/769.full.pdf
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4.
Phylogenetic Diversity on Split Networks
Open Access
Title:
Phylogenetic Diversity on Split Networks
Author:
Bui Quang Minh
;
Steffen Klaere
;
Arndt Von Haeseler
Bui Quang Minh
;
Steffen Klaere
;
Arndt Von Haeseler
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Description:
In biodiversity conservation, one is interested in selecting a subset of taxa for preservation priority. Phylogenetic diversity (PD) provides a quantitative measure for taxon selection on phylogenetic trees. In particular, PD is the total length of the minimal subtree induced by the selected taxa. Recently, it has been shown that on trees the ma...
In biodiversity conservation, one is interested in selecting a subset of taxa for preservation priority. Phylogenetic diversity (PD) provides a quantitative measure for taxon selection on phylogenetic trees. In particular, PD is the total length of the minimal subtree induced by the selected taxa. Recently, it has been shown that on trees the maximal PD score and the corresponding subset of taxa can be computed by a greedy algorithm. However, if evolution is not treelike and networks are a more appropriate illustration of phylogenetic relationships, then the greedy strategy no longer works. Here, we will extend the notion of PD to phylogenetic networks. To this end, we suggest a dynamic programming algorithm (PDNET) which guarantees the computation of optimal PD scores and PD sets for circular networks, a commonly encountered category of networks. PDNET has polynomial time complexity. Finally we apply PDNET to biological data and compare the resulting PD sets to the selection of taxa derived from a tree. The outcome indicates that it is advisable to include also nontreelike effects when dealing with conservation questions.
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Contributors:
The Pennsylvania State University CiteSeerX Archives
Year of Publication:
20110620
Source:
http://www.newton.cam.ac.uk/preprints/NI07090.pdf
http://www.newton.cam.ac.uk/preprints/NI07090.pdf
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Document Type:
text
Language:
en
Subjects:
phylogenetic diversity ; dynamic programming ; phylogenetic network
phylogenetic diversity ; dynamic programming ; phylogenetic network
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Rights:
Metadata may be used without restrictions as long as the oai identifier remains attached to it.
Metadata may be used without restrictions as long as the oai identifier remains attached to it.
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URL:
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.192.3523
http://www.newton.cam.ac.uk/preprints/NI07090.pdf
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.192.3523
http://www.newton.cam.ac.uk/preprints/NI07090.pdf
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5.
Stochastic Models of Molecular Evolution
Title:
Stochastic Models of Molecular Evolution
Author:
Klaere, Steffen
Klaere, Steffen
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Publisher:
LudwigMaximiliansUniversität München
Year of Publication:
20050708
Document Type:
Dissertation ; NonPeerReviewed
Subjects:
Fakultät für Mathematik ; Informatik und Statistik
Fakultät für Mathematik ; Informatik und Statistik
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Relations:
http://edoc.ub.unimuenchen.de/3992/
URL:
http://edoc.ub.unimuenchen.de/3992/1/Klaere_Steffen.pdf
http://nbnresolving.de/urn:nbn:de:bvb:1939922
http://edoc.ub.unimuenchen.de/3992/1/Klaere_Steffen.pdf
http://nbnresolving.de/urn:nbn:de:bvb:1939922
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University of Munich: Digital theses
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6.
Extinction in a branching process: why some of the fittest strategies cannot guarantee survival
Open Access
Title:
Extinction in a branching process: why some of the fittest strategies cannot guarantee survival
Author:
Sawaya, Sterling
;
Klaere, Steffen
Sawaya, Sterling
;
Klaere, Steffen
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Description:
Abstract Biological fitness is typically measured by the expected rate of reproduction, but strategies with high fitness can also have high probabilities of extinction. Likewise, gambling strategies with a high expected payoff can also have a high risk of ruin. We take inspiration from the gambler’s ruin problem to examine how extinction is rela...
Abstract Biological fitness is typically measured by the expected rate of reproduction, but strategies with high fitness can also have high probabilities of extinction. Likewise, gambling strategies with a high expected payoff can also have a high risk of ruin. We take inspiration from the gambler’s ruin problem to examine how extinction is related to population growth. Using moment theory we demonstrate how higher moments can impact the probability of extinction and how the first few moments can be used to find bounds on the extinction probability, focusing on s convex ordering of random variables. This approach generates “best case” and “worst case” scenarios to provide upper and lower bounds on the probability of extinction. MSC Codes 92D15, 60J80, 60E15
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Publisher:
BioMed Central Ltd.
Year of Publication:
20140616
Document Type:
Research
Language:
en
Subjects:
Extinction ; Branching process ; Sconvex
Extinction ; Branching process ; Sconvex
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Rights:
Copyright 2014 Sawaya and
Klaere
; licensee Springer.
Copyright 2014 Sawaya and
Klaere
; licensee Springer.
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URL:
http://www.jsdajournal.com/content/1/1/10
http://www.jsdajournal.com/content/1/1/10
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BioMed Central
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7.
The link between segregation and phylogenetic diversity
Open Access
Title:
The link between segregation and phylogenetic diversity
Author:
Bryant, David
;
Klaere, Steffen
Bryant, David
;
Klaere, Steffen
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Description:
We derive an invertible transform linking two widely used measures of species diversity: phylogenetic diversity and the expected proportions of segregating (nonconstant) sites. We assume a biallelic, symmetric, finite site model of substitution. Like the Hadamard transform of Hendy and Penny, the transform can be expressed completely independe...
We derive an invertible transform linking two widely used measures of species diversity: phylogenetic diversity and the expected proportions of segregating (nonconstant) sites. We assume a biallelic, symmetric, finite site model of substitution. Like the Hadamard transform of Hendy and Penny, the transform can be expressed completely independent of the underlying phylogeny. Our results bridge work on diversity from two quite distinct scientific communities. ; Comment: 14 pages, 1 figure, 12 references
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Year of Publication:
20100826
Document Type:
text
Subjects:
Quantitative Biology  Populations and Evolution ; Mathematics  Probability
Quantitative Biology  Populations and Evolution ; Mathematics  Probability
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URL:
http://arxiv.org/abs/1008.4625
http://arxiv.org/abs/1008.4625
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Content Provider:
ArXiv.org (Cornell University Library)
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8.
Extinction in a branching process: Why some of the fittest strategies cannot guarantee survival
Open Access
Title:
Extinction in a branching process: Why some of the fittest strategies cannot guarantee survival
Author:
Sawaya, Sterling
;
Klaere, Steffen
Sawaya, Sterling
;
Klaere, Steffen
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Description:
The fitness of a biological strategy is typically measured by its expected reproductive rate, the first moment of its offspring distribution. However, strategies with high expected rates can also have high probabilities of extinction. A similar situation is found in gambling and investment, where strategies with a high expected payoff can also h...
The fitness of a biological strategy is typically measured by its expected reproductive rate, the first moment of its offspring distribution. However, strategies with high expected rates can also have high probabilities of extinction. A similar situation is found in gambling and investment, where strategies with a high expected payoff can also have a high risk of ruin. We take inspiration from the gambler's ruin problem to examine how extinction is related to population growth. Using moment theory we demonstrate how higher moments can impact the probability of extinction. We discuss how moments can be used to find bounds on the extinction probability, focusing on sconvex ordering of random variables, a method developed in actuarial science. This approach generates "best case" and "worst case" scenarios to provide upper and lower bounds on the probability of extinction. Our results demonstrate that even the most fit strategies can have high probabilities of extinction. ; Comment: Best case extrema added
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Year of Publication:
20120910
Document Type:
text
Subjects:
Quantitative Biology  Populations and Evolution ; Statistics  Applications
Quantitative Biology  Populations and Evolution ; Statistics  Applications
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DDC:
519 Probabilities & applied mathematics
(computed)
URL:
http://arxiv.org/abs/1209.2074
http://arxiv.org/abs/1209.2074
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ArXiv.org (Cornell University Library)
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9.
An algebraic analysis of the two state Markov model on tripod trees
Open Access
Title:
An algebraic analysis of the two state Markov model on tripod trees
Author:
Klaere, Steffen
;
Liebscher, Volkmar
Klaere, Steffen
;
Liebscher, Volkmar
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Description:
Methods of phylogenetic inference use more and more complex models to generate trees from data. However, even simple models and their implications are not fully understood. Here, we investigate the twostate Markov model on a tripod tree, inferring conditions under which a given set of observations gives rise to such a model. This type of invest...
Methods of phylogenetic inference use more and more complex models to generate trees from data. However, even simple models and their implications are not fully understood. Here, we investigate the twostate Markov model on a tripod tree, inferring conditions under which a given set of observations gives rise to such a model. This type of investigation has been undertaken before by several scientists from different fields of research. In contrast to other work we fully analyse the model, presenting conditions under which one can infer a model from the observation or at least get support for the treeshaped interdependence of the leaves considered. We also present all conditions under which the results can be extended from tripod trees to quartet trees, a step necessary to reconstruct at least a topology. Apart from finding conditions under which such an extension works we discuss example cases for which such an extension does not work. ; Comment: 32 pages, four figures
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Year of Publication:
20101130
Document Type:
text
Subjects:
Quantitative Biology  Populations and Evolution ; Mathematics  Algebraic Geometry
Quantitative Biology  Populations and Evolution ; Mathematics  Algebraic Geometry
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DDC:
519 Probabilities & applied mathematics
(computed)
URL:
http://arxiv.org/abs/1012.0062
http://arxiv.org/abs/1012.0062
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ArXiv.org (Cornell University Library)
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10.
The impact of single substitutions on multiple sequence alignments
Open Access
Title:
The impact of single substitutions on multiple sequence alignments
Author:
Klaere, Steffen
;
Gesell, Tanja
;
von Haeseler, Arndt
Klaere, Steffen
;
Gesell, Tanja
;
von Haeseler, Arndt
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Description:
We introduce another view of sequence evolution. Contrary to other approaches, we model the substitution process in two steps. First we assume (arbitrary) scaled branch lengths on a given phylogenetic tree. Second we allocate a Poisson distributed number of substitutions on the branches. The probability to place a mutation on a branch is proport...
We introduce another view of sequence evolution. Contrary to other approaches, we model the substitution process in two steps. First we assume (arbitrary) scaled branch lengths on a given phylogenetic tree. Second we allocate a Poisson distributed number of substitutions on the branches. The probability to place a mutation on a branch is proportional to its relative branch length. More importantly, the action of a single mutation on an alignment column is described by a doubly stochastic matrix, the socalled onestep mutation matrix. This matrix leads to analytical formulae for the posterior probability distribution of the number of substitutions for an alignment column.
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Publisher:
The Royal Society
Year of Publication:
20081007
Document Type:
Text
Language:
en
Subjects:
Research Article
Research Article
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Rights:
© 2008 The Royal Society
© 2008 The Royal Society
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URL:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2607407
http://www.ncbi.nlm.nih.gov/pubmed/18852110
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2607407
http://www.ncbi.nlm.nih.gov/pubmed/18852110
http://dx.doi.org/10.1098/rstb.2008.0140
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(13) Klaere, Steffen
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