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Computing Phylogenetic Roots with Bounded Degrees and Errors
[chapter]

2001
*
Lecture Notes in Computer Science
*

In this paper, we investigate PRk under a natural restriction that the maximum

doi:10.1007/3-540-44634-6_35
fatcat:djaascihurb4tjijvqlgvjkl64
*degree*of the*phylogenetic**root*is*bounded*from above by a constant. ... This is called the*Phylogenetic*kth*Root*Problem (PRk),*and*such a tree T , if exists, is called a*phylogenetic*kth*root*of graph G. The*computational*complexity of PRk is open, except for k ≤ 4. ... Acknowledgments GL would like to thank Paul Kearney for bringing CPRk to his attention, Bin Ma*and*Jinbo Xu for many helpful discussions. ...##
###
Computing Phylogenetic Roots with Bounded Degrees and Errors

2003
*
SIAM journal on computing (Print)
*

In this paper, we investigate PRk under a natural restriction that the maximum

doi:10.1137/s0097539701389154
fatcat:ymds6cu22rd6zblxqz7ubu6tvm
*degree*of the*phylogenetic**root*is*bounded*from above by a constant. ... This is called the*Phylogenetic*kth*Root*Problem (PRk),*and*such a tree T , if exists, is called a*phylogenetic*kth*root*of graph G. The*computational*complexity of PRk is open, except for k ≤ 4. ... Acknowledgments GL would like to thank Paul Kearney for bringing CPRk to his attention, Bin Ma*and*Jinbo Xu for many helpful discussions. ...##
###
Computing phylogenetic roots with bounded degrees and errors is NP-complete

2006
*
Theoretical Computer Science
*

In the course of our proof, we will determine all trees (possibly

doi:10.1016/j.tcs.2006.06.016
fatcat:5bga3s3wkvdxvetl6ifahwq7fe
*with**degree*2 nodes) that approximate the (s (k) − 1)-clique by*errors*at most 2. ... In this paper we study the*computational*complexity of the following optimization problem: given a graph G = (V , E), we wish to find a tree T such that (1) the*degree*of each internal node of T is at ... kth*root*T*with*at most*errors*. ...##
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Page 5074 of Mathematical Reviews Vol. , Issue 2004f
[page]

2004
*
Mathematical Reviews
*

*roots*

*with*

*bounded*

*degrees*

*and*

*errors*. ... In this paper, the authors investigate PRA under a natural restriction that the maximum

*degree*of the

*phylogenetic*

*root*is

*bounded*from above by a constant. ...

##
###
Polytomies and Phylogenetically Independent Contrasts: Examination of the Bounded Degrees of Freedom Approach

1999
*
Systematic Biology
*

We speci cally tested the adequacy of

doi:10.1080/106351599260139
pmid:12066293
fatcat:fca3ly2mw5ck5irc477xxeds6i
*bounding**degrees*of freedom, as suggested by Purvis*and*Garland (1993; Syst. Biol. 42:569-575). ... Overall,*and*irrespective of evolutionary model,*degrees*of freedom were appropriately*bounded*for hypothesis testing,*and*unbiased estimates of the correlation coef cient were obtained. ... Bleiweiss*and*J. A. W. Kirsch for providing*phylogenetic*trees, C. Lázaro-Perea for comments on a previous version of the manuscript,*and*A. ...##
###
Constructing Optimal Trees from Quartets

2001
*
Journal of Algorithms
*

The main result is an algorithm for determining

doi:10.1006/jagm.2000.1133
fatcat:x3g3mnbb6vbapi3oui26entabu
*bounded**degree*trees*with*optimal quartet weight, subject to the constraint that the splits in the tree come from a given collection, for example, the splits ... The problem is central to divide*and*conquer approaches to*phylogenetic*analysis*and*has been receiving considerable attention from the*computational*biology community. ... Semple*and*V. Berry for help*with*proof reading. ...##
###
Robinson-Foulds Reticulation Networks
[article]

2019
*
bioRxiv
*
pre-print

RF-Net was able to estimate a large

doi:10.1101/642793
fatcat:dtyox5djavfujlf3j3nucnbptu
*and*credible reassortment network*with*164 taxa. ... Using simulations we experimentally validate the ability of our method, RF-Net, to reconstruct correct*phylogenetic*networks in the presence of*error*in input data. ... A (*phylogenetic*) network is a directed acyclic graph (DAG)*with*a designated*root*vertex of in-*degree*zero*and*all other vertices are either of in-*degree*one*and*out-*degree*two (tree vertices), in-*degree*...##
###
Computing the maximum agreement of phylogenetic networks

2005
*
Theoretical Computer Science
*

*with*indegree 2. ... We prove that the problem is NPhard even if restricted to three

*phylogenetic*networks

*and*give an O(n 2 )-time algorithm for the special case of two level-1

*phylogenetic*networks, where n is the number ... Note that this is O(n log n) for two trees

*with*maximum

*degree*

*bounded*by a constant

*and*O(n 1.5 ) for two trees

*with*unbounded

*degrees*. ...

##
###
Computing the Maximum Agreement of Phylogenetic Networks

2004
*
Electronical Notes in Theoretical Computer Science
*

*with*indegree 2. ... We prove that the problem is NPhard even if restricted to three

*phylogenetic*networks

*and*give an O(n 2 )-time algorithm for the special case of two level-1

*phylogenetic*networks, where n is the number ... Note that this is O(n log n) for two trees

*with*maximum

*degree*

*bounded*by a constant

*and*O(n 1.5 ) for two trees

*with*unbounded

*degrees*. ...

##
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On the Inference of Large Phylogenies with Long Branches: How Long Is Too Long?

2010
*
Bulletin of Mathematical Biology
*

The accurate reconstruction of phylogenies from short molecular sequences is an important problem in

doi:10.1007/s11538-010-9584-6
pmid:20931293
fatcat:bfjxipzjnvhsxkr5zna2jvnjea
*computational*biology. ... Here, we consider a more general evolutionary model, the GTR model, where the q × q rate matrix Q is reversible*with*q ≥ 2. For this model, recent results of Roch E. ... the original author(s)*and*source are credited. ...##
###
Evaluation of ultrametric phylogenetic tree estimation

2020
*
Journal of the Korean Data and Information Science Society
*

The three parameterizations, called relAge, Thorne,

doi:10.7465/jkdi.2020.31.3.663
fatcat:3hfxp4fabvfyzc4n5s2pru474q
*and*Rambaut, were found to be correctly estimated in most cases, although the relAge parameterization resulted in tree estimation*with*zero-length branches ... A*phylogenetic*tree is a tree-like graphical representation of the evolutionary history of a group of organisms. ... The*bound*on the*root*-age can also be enforced by log transformation. ...##
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On the inference of large phylogenies with long branches: How long is too long?
[article]

2010
*
arXiv
*
pre-print

Here, we show that this phenomenon also holds for

arXiv:1001.3480v1
fatcat:5wklttmz6zgdfkx53azn2fvfjq
*phylogenetic*reconstruction by exhibiting a family of symmetric models Q*and*a*phylogenetic*reconstruction algorithm which recovers the tree from O( n) ... For this model, recent results of [Roch'09] show that the tree can be accurately reconstructed*with*sequences of length O((n)) when the branch lengths are below , known as the Kesten-Stigum (KS)*bound*. ... Proposition 1 shows that this "*error*channel" is of the Potts type*with**bounded*length, no matter how deep the tree. ...##
###
A reduction algorithm for computing the hybridization number of two trees

2007
*
Evolutionary Bioinformatics
*

Although the two-tree problem is NP-hard, our algorithm always gives the exact solution

pmid:19461978
pmcid:PMC2684132
fatcat:kuqoq7l2hjespphfc2iv3jshz4
*and*runs efficiently on many real biological problems. ... Previous algorithms for the two-tree problem either solve a restricted version of the problem or give an answer*with*no guarantee of the closeness to the exact solution. ... Acknowledgment The authors thank Heiko Schmidt for providing them*with*the reconstructed gene trees of the grass data set. ...##
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Fast and accurate inference of phylogenetic networks using large-scale genomic sequence data
[article]

2017
*
bioRxiv
*
pre-print

The answer to this fundamental question not only depends upon densely sampled

doi:10.1101/132795
fatcat:zhagnarpv5agrbhvvbfopzdhja
*and*divergent genomic sequence data, but also*computational*methods which are capable of accurately*and*efficiently inferring ... We conduct a performance study involving a range of evolutionary scenarios,*and*we demonstrate that FastNet outperforms state-of-the-art methods in terms of*computational*efficiency*and*topological accuracy ... CCF-1565719 (to KJL), CCF-1714417 (to KJL),*and*DEB-1737898 (to GMB*and*KJL), BEACON grants (NSF STC Cooperative Agreement DBI-093954) to GMB*and*KJL,*and**computing*resources provided by MSU HPCC. ...##
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Comparison of Tree-Child Phylogenetic Networks
[article]

2007
*
arXiv
*
pre-print

Simple, polynomial algorithms for reconstructing a tree-child

arXiv:0708.3499v1
fatcat:w7n77mmgznds5gicayk3pmz3m4
*phylogenetic*network from its path multiplicity vectors, for*computing*the distance between two tree-child*phylogenetic*networks,*and*for aligning ... a pair of tree-child*phylogenetic*networks, are provided,*and*they have been implemented as a Perl package*and*a Java applet,*and*they are available at http://bioinfo.uib.es/~recerca/phylonetworks/mudistance ... -C02-01,*and*by EU project INTAS IT 04-77-7178. ...
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