Results 1  10
of
15,369
Counting ancestral reconstructions in a fixed phylogeny
"... We give formulas for calculating in polynomial time the number of ancestral reconstructions for a tree with binary leaf and root labels for each number of 0 → 1 and 1 → 0 arcs. For trees of fixed degree, the corresponding numbers of 0 → 0and 1 → 1 arcs can be deduced. We calculate intervals for the ..."
Abstract
 Add to MetaCart
We give formulas for calculating in polynomial time the number of ancestral reconstructions for a tree with binary leaf and root labels for each number of 0 → 1 and 1 → 0 arcs. For trees of fixed degree, the corresponding numbers of 0 → 0and 1 → 1 arcs can be deduced. We calculate intervals
Breakpoint phylogenies
, 1997
"... We describe a number of heuristics for inferring the gene orders of the hypothetical ancestral genomes in a fixed phylogeny. The optimization criterion is the minimum number of breakpoints (pairs of genes adjacent in one genome but not the other) in the gene orders of two genomes connected byanedge ..."
Abstract

Cited by 70 (4 self)
 Add to MetaCart
We describe a number of heuristics for inferring the gene orders of the hypothetical ancestral genomes in a fixed phylogeny. The optimization criterion is the minimum number of breakpoints (pairs of genes adjacent in one genome but not the other) in the gene orders of two genomes connected byanedge
Two Strikes Against Perfect Phylogeny
 PROC. OF 19TH INTERNATIONAL COLLOQUIUM ON AUTOMATA LANGUAGES AND PROGRAMMING
, 1992
"... One of the major efforts in molecular biology is the computation of phylo genies for species sets. A longstanding open problem in this area is called the Perfect Phylogeny problem. For almost two decades the complexity of this problem remained open, with progress limited to polynomial time algor ..."
Abstract

Cited by 123 (28 self)
 Add to MetaCart
algorithms for a few special cases, and many relaxations of the problem shown to be NPComplete. From an applications point of view, the problem is of interest both in its general forin, where the number of characters may vary, and in its fixedparameter form. The Perfect Phylogeny problem has been shown
A PolynomialTime Algorithm for the Perfect Phylogeny Problem when the Number of Character States Is Fixed
 SIAM JOURNAL ON COMPUTING
, 1994
"... We present a polynomialtime algorithm for determining whether a set of species, described by the characters they exhibit, has a perfect phylogeny, assuming the maximum number of possible states for a character is fixed. This solves a longstanding open problem. Our result should be contrasted with ..."
Abstract

Cited by 62 (4 self)
 Add to MetaCart
We present a polynomialtime algorithm for determining whether a set of species, described by the characters they exhibit, has a perfect phylogeny, assuming the maximum number of possible states for a character is fixed. This solves a longstanding open problem. Our result should be contrasted
molecular phylogenies
"... This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal noncommercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or sel ..."
Abstract
 Add to MetaCart
This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal noncommercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier’s archiving and manuscript policies are encouraged to visit:
Perfect path phylogeny haplotyping with missing data is fixedparameter tractable
 In First International Workshop on Parametrized and Exact Computation (IWPEC 2004
, 2004
"... Abstract. Haplotyping via perfect phylogeny is a method for retrieving haplotypes from genotypes. Fast algorithms are known for computing perfect phylogenies from complete and errorfree input instances—these instances can be organized as a genotype matrix whose rows are the genotypes and whose colu ..."
Abstract

Cited by 5 (2 self)
 Add to MetaCart
corresponding perfect phylogeny has to be a path. Secondly, we assume that the number of missing entries in every column of the input genotype matrix is bounded. We show that the perfect path phylogeny haplotyping problem is fixedparameter tractable when we consider the maximum number of missing entries per
Breakpoint Medians and Breakpoint Phylogenies: A FixedParameter Approach
, 2002
"... With breakpoint distance, the genome rearrangement field delivered one of the currently most popular measures in phylogenetic studies for related species. Here, BREAK POINT MEDIAN, which is NPcomplete already for three given species (whose genomes are represented as signed orderings), is the core ..."
Abstract

Cited by 4 (1 self)
 Add to MetaCart
basic problem. For the important special case of three species, approximation (ratio 7/6) and exact heuristic algorithms were developed. Here, we provide an exact, fixedparameter algorithm with provable performance bounds. For instance, a breakpoint median for three signed orderings over n elements
A Faster Algorithm for the Perfect Phylogeny Problem when the Number of Characters is Fixed
, 1994
"... We present an algorithm for determining whether a set of species, described by the characters they exhibit, has a perfect phylogeny, assuming the maximum number of characters is fixed. This algorithm is simpler and faster than the known algorithms when the number of characters is at least 4. 1 Intro ..."
Abstract
 Add to MetaCart
We present an algorithm for determining whether a set of species, described by the characters they exhibit, has a perfect phylogeny, assuming the maximum number of characters is fixed. This algorithm is simpler and faster than the known algorithms when the number of characters is at least 4. 1
FixedParameter Algorithms In Phylogenetics
, 2007
"... We survey the use of fixedparameter algorithms in the field of phylogenetics, which is the study of evolutionary relationships. The central problem in phylogenetics is the reconstruction of the evolutionary history of biological species, but its methods also apply to linguistics, philology or archi ..."
Abstract

Cited by 11 (1 self)
 Add to MetaCart
We survey the use of fixedparameter algorithms in the field of phylogenetics, which is the study of evolutionary relationships. The central problem in phylogenetics is the reconstruction of the evolutionary history of biological species, but its methods also apply to linguistics, philology
Results 1  10
of
15,369