Scalable molecular dynamics with NAMD | Journal of Computational Chemistry | 2005 | 12.7K |
Haploview: analysis and visualization of LD and haplotype maps | Bioinformatics | 2005 | 11.8K |
GROMACS: fast, flexible, and free | Journal of Computational Chemistry | 2005 | 10.3K |
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research | Bioinformatics | 2005 | 8.2K |
The Amber biomolecular simulation programs | Journal of Computational Chemistry | 2005 | 6.2K |
PLS path modeling | Computational Statistics and Data Analysis | 2005 | 3.1K |
BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks | Bioinformatics | 2005 | 3.1K |
A general framework for weighted gene co-expression network analysis | Statistical Applications in Genetics and Molecular Biology | 2005 | 3K |
PowerMarker: an integrated analysis environment for genetic marker analysis | Bioinformatics | 2005 | 2.9K |
ProtTest: selection of best-fit models of protein evolution | Bioinformatics | 2005 | 2.6K |
HyPhy: hypothesis testing using phylogenies | Bioinformatics | 2005 | 2.1K |
ROCR: visualizing classifier performance in R | Bioinformatics | 2005 | 2K |
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary | Bioinformatics | 2005 | 1.9K |
Protein homology detection by HMM-HMM comparison | Bioinformatics | 2005 | 1.9K |
MatInspector and beyond: promoter analysis based on transcription factor binding sites | Bioinformatics | 2005 | 1.7K |
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content | Bioinformatics | 2005 | 1.6K |
GMAP: a genomic mapping and alignment program for mRNA and EST sequences | Bioinformatics | 2005 | 1.4K |
SNOPT: An SQP Algorithm for Large-Scale Constrained Optimization | SIAM Review | 2005 | 1.3K |
ACT: the Artemis Comparison Tool | Bioinformatics | 2005 | 1.3K |
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees | Bioinformatics | 2005 | 1.2K |
Use of within-array replicate spots for assessing differential expression in microarray experiments | Bioinformatics | 2005 | 1.1K |
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis | Bioinformatics | 2005 | 1.1K |
GMD@CSB.DB: the Golm Metabolome Database | Bioinformatics | 2005 | 1.1K |
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments | Bioinformatics | 2005 | 1.1K |
De novo identification of repeat families in large genomes | Bioinformatics | 2005 | 1K |