• GenRGenS

  • Referenced in 7 articles [sw09070]
  • useful for sequence analysis, such as Markov chains, hidden Markov models, weighted context-free grammars...
  • HMM-Fisher

  • Referenced in 4 articles [sw28769]
  • data. This approach first uses a hidden Markov chain to model the methylation signals...
  • ESMERALDA

  • Referenced in 5 articles [sw25968]
  • sequences). It supports continuous density Hidden Markov models, Markov chain (N-gramm) models, and Gaussian...
  • MARCH

  • Referenced in 1 article [sw26385]
  • types of Markovian models including homogeneous Markov Chains, Hidden Markov Models (HMMs) and Double Chain...
  • RJaCGH

  • Referenced in 1 article [sw14653]
  • Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models. The selection of the number...
  • PMT

  • Referenced in 0 articles [sw29885]
  • probabilistic models: Gaussian mixtures, Factor analyzers, Markov chains, Hidden Markov models, and Linear dynamic systems...
  • iHMMune-align

  • Referenced in 2 articles [sw23147]
  • iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin ... gene sequences. MOTIVATION: Immunoglobulin heavy chain (IGH) genes in mature B lymphocytes are the result ... alignment program that uses a hidden Markov model (HMM) to model the processes involved...
  • Sulfinator

  • Referenced in 3 articles [sw35758]
  • prediction of tyrosine sulfation sites in polypeptide chains. The Sulfinator is a software tool that ... overall accuracy of 98%. Four different Hidden Markov Models were constructed, each of them specialized...
  • Venture

  • Referenced in 9 articles [sw14670]
  • models that do inference over latent variables hidden from Venture. Second, we describe probabilistic execution ... blocked proposals based on particle Markov chain Monte Carlo and mean-field variational inference techniques...
  • SoDA2

  • Referenced in 3 articles [sw23149]
  • SoDA2, which is based on a Hidden Markov Model and used to compute the posterior ... group of randomly selected Ig heavy chains from Genbank. In most tests, SoDA2 performed better...
  • EasyGene

  • Referenced in 7 articles [sw17322]
  • gene finder is based on a hidden Markov model (HMM) that is automatically estimated ... sense of a third order Markov chain. Conclusions: The result is a flexible gene finder...
  • iBATCGH

  • Referenced in 1 article [sw19388]
  • observed surrogate CGH measurement via a hidden Markov model. Selection of relevant associations is performed ... Posterior inference is carried out through Markov chain Monte Carlo techniques that efficiently explores...
  • HmmSeq

  • Referenced in 1 article [sw13742]
  • data. Our novel hmmSeq methodology uses hidden Markov models to account for potential co-expression ... hmmSeq model, we develop an efficient Markov chain Monte Carlo algorithm. Further, we develop...
  • repgenHMM

  • Referenced in 1 article [sw34133]
  • sequence data. Results: We present a Hidden Markov model, which accounts for all plausible scenarios ... data for both the alpha and beta chains of the T cell receptor. To test...
  • FORESST

  • Referenced in 3 articles [sw26866]
  • sequence based on a combination of hidden Markov models (HMMs) and secondary structure prediction ... helices, strands and coils along the polypeptide chain. When a more extensive library of HMMs...
  • ADOL-C

  • Referenced in 249 articles [sw00019]
  • ADOL-C: Automatic Differentiation of C/C++. We present...
  • CoCoA

  • Referenced in 654 articles [sw00143]
  • CoCoA is a system for Computations in Commutative...
  • GAUSS

  • Referenced in 119 articles [sw00322]
  • The GAUSS Mathematical and Statistical System is a...
  • KNITRO

  • Referenced in 196 articles [sw00490]
  • KNITRO is a solver for nonlinear optimization. It...
  • Macaulay2

  • Referenced in 1904 articles [sw00537]
  • Macaulay2 is a software system devoted to supporting...