• 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...