Biology

Proc. Natl. Acad. Sci. USA Vol. 85, pp. 2444-2448, April 1988 Biochemistry ... (amino acid/nucleic acid/data base searches/local similarity) ... WILLIAM R. PEARSON* AND DAVID J. LIPMANt ... *Department of Biochemistry, University of Virginia, Charlottesville, VA 22908; and ...

Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%. I...

Genome-wide association studies have identified hundreds of genetic variants associated with complex human diseases and traits, and have provided valuable insights into their genetic architecture. Most variants identified so far confer relatively small increments in risk, and ...

Alzheimer's disease causes dementia in many elderly people and in some individu-als with Down syndrome who survive to age 50. Alzheimer's is characterized by various pathological markers in the brain-large numbers of amyloid plaques surrounded by neurons ...

Development of the acute and chronic inflammatory responses known as gout and pseudogout are associated with the deposition of monosodium urate (MSU) or calcium pyrophosphate dihydrate (CPPD) crystals, respectively, in joints and periarticular tissues. Although MSU crystals ...