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WABI
2005
Springer
120views Bioinformatics» more  WABI 2005»
13 years 10 months ago
A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance
Phylogenetic tree searching algorithms often produce thousands of trees which biologists save in Newick format in order to perform further analysis. Unfortunately, Newick is neithe...
Robert S. Boyer, Warren A. Hunt Jr., Serita M. Nel...
IPPS
2006
IEEE
13 years 11 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...
EUROCAST
2009
Springer
185views Hardware» more  EUROCAST 2009»
13 years 12 months ago
Solving the Euclidean Bounded Diameter Minimum Spanning Tree Problem by Clustering-Based (Meta-)Heuristics
The bounded diameter minimum spanning tree problem is an NP-hard combinatorial optimization problem arising in particular in network design. There exist various exact and metaheuri...
Martin Gruber, Günther R. Raidl
GECCO
2009
Springer
143views Optimization» more  GECCO 2009»
13 years 12 months ago
Exploiting hierarchical clustering for finding bounded diameter minimum spanning trees on euclidean instances
The bounded diameter minimum spanning tree problem is an NP-hard combinatorial optimization problem arising, for example, in network design when quality of service is of concern. ...
Martin Gruber, Günther R. Raidl
BMCBI
2006
161views more  BMCBI 2006»
13 years 5 months ago
A novel approach to phylogenetic tree construction using stochastic optimization and clustering
Background: The problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational bi...
Ling Qin, Yixin Chen, Yi Pan, Ling Chen