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» Heuristics for the Phylogeny Problem
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BIBE
2007
IEEE
127views Bioinformatics» more  BIBE 2007»
14 years 2 months ago
A Heuristic for Phylogenetic Reconstruction Using Transposition
Abstract—Because of the advent of high-throughput sequencing and the consequent reduction in cost of sequencing, many organisms have been completely sequenced and most of their g...
Feng Yue, Meng Zhang, Jijun Tang
STOC
2005
ACM
84views Algorithms» more  STOC 2005»
14 years 8 months ago
Learning nonsingular phylogenies and hidden Markov models
In this paper, we study the problem of learning phylogenies and hidden Markov models. We call the Markov model nonsingular if all transtion matrices have determinants bounded away...
Elchanan Mossel, Sébastien Roch
RECOMB
2004
Springer
14 years 8 months ago
Perfect phylogeny and haplotype assignment
This paper is concerned with the reconstruction of perfect phylogenies from binary character data with missing values, and related problems of inferring complete haplotypes from h...
Eran Halperin, Richard M. Karp
JPDC
2006
112views more  JPDC 2006»
13 years 7 months ago
Large scale multiple sequence alignment with simultaneous phylogeny inference
Multiple sequence alignment (MSA) and phylogenetic tree reconstruction are one of the most important problems in the computational biology. While both these problems are of great ...
Gilles Parmentier, Denis Trystram, Jaroslaw Zola
IPPS
2006
IEEE
14 years 1 months ago
Parallel multiple sequence alignment with local phylogeny search by simulated annealing
The problem of multiple sequence alignment is one of the most important problems in computational biology. In this paper we present a new method that simultaneously performs multi...
Jaroslaw Zola, Denis Trystram, Andrei Tchernykh, C...