• ClustalW

  • Referenced in 138 articles [sw12016]
  • alignment through sequence weighting, position-specific gap penalties and weight matrix choice...
  • Quicksort

  • Referenced in 183 articles [sw20694]
  • sorting algorithms available, as testified by the choice of Quicksort as the default sorting algorithm ... number of inversions in the input sequence. This result provides a theoretical explanation...
  • PSIPRED

  • Referenced in 15 articles [sw11340]
  • submit a protein sequence, perform a prediction of their choice and receive the results ... three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction...
  • HTSeq

  • Referenced in 8 articles [sw16898]
  • work with high-throughput sequencing data. Motivation: A large choice of tools exists for many...
  • DIYABC

  • Referenced in 9 articles [sw21021]
  • from microsatellite and DNA sequence data, (ii) efficient Bayesian model choice using linear discriminant analysis...
  • DAFS

  • Referenced in 1 article [sw17125]
  • aligned sequences is a better choice if homologous sequences with reliable alignments are available. However...
  • Whittle Surrogate

  • Referenced in 1 article [sw22532]
  • number of remaining sequences given that choice. The number of possible symbol sequences is given...
  • MaCH

  • Referenced in 7 articles [sw17274]
  • other and uses available genotype and shotgun sequence data to estimate unobserved genotypes and haplotypes ... evaluate its accuracy and utility, considering choices of genotyping panels, reference panel configurations, and designs ... where genotyping is replaced with shotgun sequencing. Importantly, we show that genotype imputation not only...
  • MicroRazerS

  • Referenced in 2 articles [sw34361]
  • reads. Motivation: Deep sequencing has become the method of choice for determining the small...
  • HHpred

  • Referenced in 7 articles [sw17271]
  • HMMs). It allows to search a wide choice of databases, such as the PDB, SCOP ... accepts a single query sequence or a multiple alignment as input. Within only...
  • nucleoSim

  • Referenced in 1 article [sw22391]
  • reverse reads emulating next-generation sequencing. The user has choice between three different distributions...
  • qLearn

  • Referenced in 20 articles [sw11117]
  • optimal dynamic regime. We propose an adaptive choice of m and show that it produces ... Archive Network (http://cran.r-project.org/). Analysis of the Sequenced Treatment Alternatives to Relieve Depression (STAR...
  • BADER

  • Referenced in 1 article [sw20384]
  • Differential Expression in RNA-sequencing data (BADER). Due to our choice of data and prior...
  • SQLNet

  • Referenced in 1 article [sw42256]
  • sequence-to-sequence-style model is sensitive to the choice from one of them. This ... fundamentally solve this problem by avoiding the sequence-to-sequence structure when the order does...
  • CONTRAfold

  • Referenced in 8 articles [sw17117]
  • have been the dominant strategy for single sequence RNA secondary structure prediction. More recently, stochastic ... energy minimization methods as the tool of choice for secondarystructure prediction, as the accuracies ... thermodynamic models, CONTRAfold achieves the highest single sequence prediction accuracies to date, outperforming currently available...
  • gglogo

  • Referenced in 0 articles [sw15659]
  • Sequence Plots. Visualize sequences in (modified) logo plots. The design choices used by these logo...
  • MU-CSeq

  • Referenced in 3 articles [sw25257]
  • nondeterministic guess) the sequence of write operations in the shared memory and then simulate ... according to any scheduling that respects this choice. Simulation is done thread-by-thread...
  • dSTEM

  • Referenced in 3 articles [sw36073]
  • power consistency, as the length of the sequence and the size of the jumps ... asymptotic conditions and guide the choice of smoothing bandwidth. The methods are illustrated in magnetometer...
  • MaChAmp

  • Referenced in 1 article [sw33965]
  • Massive Choice, Ample Tasks (MaChAmp): A Toolkit for Multi-task Learning in NLP. Transfer learning ... uniform toolkit, from text classification to sequence labeling and dependency parsing...
  • TOPALi

  • Referenced in 1 article [sw30327]
  • that allows the user to identify recombinant sequences within a DNA multiple alignment (either automatically ... manual investigation). TOPALi allows a choice of three statistical methods to predict the positions ... then used to identify putative recombinant sequences and their relationships to other sequences. In addition...