• REPuter

• Referenced in 17 articles [sw29724]
• applications of repeat analysis on a genomic scale. The repetitive structure of genomic DNA holds ... genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein...

• FatiGO

• Referenced in 21 articles [sw12318]
• genes within the context of a genome-scale experiment (DNA microarray, proteomics, etc.). Said procedure...

• BiGG

• Referenced in 10 articles [sw17247]
• large scale metabolic reconstructions. Background: Genome-scale metabolic reconstructions under the Constraint Based Reconstruction ... Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome...

• ranger

• Referenced in 42 articles [sw14498]
• analyze data on the scale of a genome-wide association study...

• Notung

• Referenced in 13 articles [sw08917]
• Duplications and Optimizing Gene Family Tree. Large scale gene duplication is a major force driving ... evolution of genetic functional innovation. Whole genome duplications are widely believed to have played ... soon allow similar studies on a genomic scale, but such studies will be limited unless...

• pi-MASS

• Referenced in 20 articles [sw17249]
• selection regression for genome-wide association studies and other large-scale problems We consider applying ... studies and similar large-scale regression problems. Currently, typical genome-wide association studies measure hundreds ... issue of “missing heritability” in genome-wide association studies. More generally, we demonstrate that, despite ... provide useful inferences in these large-scale problems, and in our simulations produces better power...

• COBRA Toolbox

• Referenced in 13 articles [sw32083]
• variety of metabolic phenotypes using genome-scale biochemical networks...

• Galaxy

• Referenced in 12 articles [sw16927]
• Galaxy: A platform for interactive large-scale genome analysis. Accessing and analyzing the exponentially expanding...

• TM4

• Referenced in 12 articles [sw26846]
• studying gene expression on a genomic scale. Advances in the precision of array printers...

• GAGE

• Referenced in 11 articles [sw13528]
• evaluation of the very latest large-scale genome assembly algorithms. We have organized this ”bake...

• BaCelLo

• Referenced in 9 articles [sw17174]
• subcellular location of proteins in large scale genomic projects. Results. BaCelLo is a predictor...

• PLINK

• Referenced in 68 articles [sw04581]
• whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses...

• Needles

• Referenced in 8 articles [sw41472]
• Needles: Toward Large-Scale Genomic Prediction with Marker-by-Environment Interaction. Genomic prediction relies ... computational resources needed for analyzing large-scale trial data. A high-performance computing solution, called...

• MSOAR

• Referenced in 7 articles [sw29658]
• between closely related species on a genome scale. It attempts to reconstruct the evolutionary history...

• MUMMER

• Referenced in 41 articles [sw17256]
• scale DNA and protein sequences. MUMmer is a system for rapidly aligning entire genomes, whether...

• CMfinder

• Referenced in 6 articles [sw17265]
• coding RNAs and computational advances in genome-scale RNA search create a need for tools...

• MetExplore

• Referenced in 4 articles [sw12274]
• allows to build, curate and analyse genome-scale metabolic networks. MetExplore stores metabolic networks ... identify compounds from masses. Several genome-scale models designed for Flux Balance Analysis have also...

• F2c2

• Referenced in 3 articles [sw17352]
• computation of flux coupling in gen ome-scale metabolic networks. Background: Flux coupling analysis ... constraint-based analysis of genome-scale metabolic networks. FCA allows detecting dependencies between reaction fluxes ... approaches. As a consequence, FCA of genome-scale metabolic networks can now be performed ... computation of flux coupling in genome-scale metabolic networks. F2C2 is freely available...

• DupTree

• Referenced in 5 articles [sw12376]
• DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Summary: DupTree ... parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users...

• EBSeq

• Referenced in 8 articles [sw17161]
• their corresponding isoforms on a genome-wide scale. However, statistical methods are required to ensure...