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» Algorithms for phylogenetic footprinting
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JACM
2006
99views more  JACM 2006»
13 years 8 months ago
Finding a maximum likelihood tree is hard
Abstract. Maximum likelihood (ML) is an increasingly popular optimality criterion for selecting evolutionary trees [Felsenstein 1981]. Finding optimal ML trees appears to be a very...
Benny Chor, Tamir Tuller
BMCBI
2005
198views more  BMCBI 2005»
13 years 8 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....
BMCBI
2004
196views more  BMCBI 2004»
13 years 8 months ago
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Background: In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUS...
Robert C. Edgar
JCB
2000
101views more  JCB 2000»
13 years 8 months ago
Evaluation Measures of Multiple Sequence Alignments
Multiple sequence alignments (MSAs) are frequently used in the study of families of protein sequences or DNA/RNA sequences. They are a fundamental tool for the understanding of th...
Gaston H. Gonnet, Chantal Korostensky, Steven A. B...
ICS
2004
Tsinghua U.
14 years 1 months ago
Applications of storage mapping optimization to register promotion
Storage mapping optimization is a flexible approach to folding array dimensions in numerical codes. It is designed to reduce the memory footprint after a wide spectrum of loop tr...
Patrick Carribault, Albert Cohen