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BMCBI
2008
104views more  BMCBI 2008»
14 years 9 months ago
Comparison of methods for estimating the nucleotide substitution matrix
Background: The nucleotide substitution rate matrix is a key parameter of molecular evolution. Several methods for inferring this parameter have been proposed, with different math...
Maribeth Oscamou, Daniel McDonald, Von Bing Yap, G...
BMCBI
2005
198views more  BMCBI 2005»
14 years 9 months ago
Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural
Background: The sequencing of the human genome has enabled us to access a comprehensive list of genes (both experimental and predicted) for further analysis. While a majority of t...
Qicheng Ma, Gung-Wei Chirn, Richard Cai, Joseph D....
IPPS
2009
IEEE
15 years 4 months ago
Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA
Computing large multiple protein sequence alignments using progressive alignment tools such as ClustalW requires several hours on state-of-the-art workstations. ClustalW uses a th...
Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
GECCO
2006
Springer
167views Optimization» more  GECCO 2006»
15 years 1 months ago
Estimating the destructiveness of crossover on binary tree representations
In some cases, evolutionary algorithms represent individuals as typical binary trees with n leaves and n-1 internal nodes. When designing a crossover operator for a particular rep...
Luke Sheneman, James A. Foster
BMCBI
2010
95views more  BMCBI 2010»
14 years 9 months ago
Heuristics for the inversion median problem
Background: The study of genome rearrangements has become a mainstay of phylogenetics and comparative genomics. Fundamental in such a study is the median problem: given three geno...
Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M. S...