• BFAST

  • Referenced in 4 articles [sw20962]
  • great importance, but equally important is maintaining alignment accuracy of short reads ... range, in the presence of errors and true biological variation. Methodology: We introduce ... freely available implementation, BFAST, which can align data produced by any of current sequencing platforms ... greater sensitivity of alignment in the context of errors and true variants, especially insertions...
  • Rose

  • Referenced in 8 articles [sw16613]
  • process, the `true’ history is logged and the `correct’ multiple sequence alignment is created simultaneously...
  • HHCART

  • Referenced in 4 articles [sw38489]
  • parallel splits. When the true decision boundaries are not aligned with the feature axes, this...
  • PathBLAST

  • Referenced in 8 articles [sw29737]
  • basic method searches for high-scoring alignments between pairs of protein interaction paths, for which ... second path. This technique discriminates between true- and false-positive interactions and allows for functional...
  • PSICOV

  • Referenced in 6 articles [sw17010]
  • identifying correlated mutations within multiple sequence alignments (MSAs), most commonly through the information-theoretic approach ... These predictions are often inaccurate because the true covariation signal in the MSA is often...
  • CUSHAW

  • Referenced in 2 articles [sw34349]
  • have motivated the development of various aligners for very short reads, typically less than ... have higher sequencing error rates and more true mutations (including substitutions, insertions, or deletions ... genome. Such new characteristics make inefficient the aligners, which are optimized for very short reads...
  • DACTAL

  • Referenced in 2 articles [sw29613]
  • datasets without ever needing to estimate an alignment on the entire dataset. DACTAL combines iteration ... that DACTAL is guaranteed to produce the true tree under certain conditions. We compare DACTAL ... SATé and maximum likelihood trees on estimated alignments using simulated and real datasets with...
  • EFICAz

  • Referenced in 3 articles [sw35281]
  • enzyme family that discriminate between true and false members of the family) identification, we have ... information from homofunctional and heterofunctional multiple sequence alignments associated with an enzyme family. The FDRs...
  • PHAT

  • Referenced in 3 articles [sw17270]
  • twilight zone, where low-scoring true positives have scores indistinguishable from high-scoring false positives ... help improve the accuracy of sequence alignments and evolutionary trees of membrane proteins. Availability...
  • GeneMarkS

  • Referenced in 6 articles [sw23024]
  • absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper ... coding regions and the Gibbs sampling multiple alignment program. GeneMarkS predicted precisely...
  • svclassify

  • Referenced in 1 article [sw33141]
  • calls. Calculates annotations from one or more aligned bam files from many high-throughput sequencing ... classify candidate structural variants (SVs) as likely true or false positives. SVClassify method gives...
  • deFuse

  • Referenced in 1 article [sw38447]
  • ends of known exons, deFuse considers all alignments and all possible locations for fusion boundaries ... approach, we curated a list of 60 true positive and 61 true negative fusion sequences...
  • Coq

  • Referenced in 1856 articles [sw00161]
  • Coq is a formal proof management system. It...
  • Mathematica

  • Referenced in 6235 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • R

  • Referenced in 9188 articles [sw00771]
  • R is a language and environment for statistical...
  • STATISTICA

  • Referenced in 37 articles [sw00913]
  • Since 1984, StatSoft has been developing the STATISTICA...
  • MIRA

  • Referenced in 1 article [sw02392]
  • MIRA is a multi-pass DNA sequence data...
  • MINITAB

  • Referenced in 204 articles [sw02865]
  • Analyze your data and improve your products and...
  • CUDA

  • Referenced in 1288 articles [sw03258]
  • The NVIDIA® CUDA® Toolkit provides a comprehensive development...
  • UCI-ml

  • Referenced in 3266 articles [sw04074]
  • UC Irvine Machine Learning Repository. We currently maintain...