• MNM

  • Referenced in 39 articles [sw06075]
  • based on the identity score, spatial sign score and spatial rank score. The methods include...
  • CLUSTAL

  • Referenced in 17 articles [sw12750]
  • nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from ... matrix of all pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. Then ... order of branching in the tree. The method is sufficiently fast and economical with memory...
  • IntScore

  • Referenced in 2 articles [sw29322]
  • network topology- and annotation-based confidence scoring methods. It also enables the integration of scores...
  • NESTOR

  • Referenced in 27 articles [sw22096]
  • them is the use of knowledge-based methods within a formal probability theory framework ... three tasks, and the details of the methods used to address them. In addition ... results of an evaluation of the hypothesis scoring and search techniques are presented and discussed...
  • LAS

  • Referenced in 18 articles [sw17180]
  • exploratory analysis of high dimensional data. Biclustering methods search for sample-variable associations ... driven by a Bonferroni-based significance score that effectively trades off between submatrix size ... compare it with a number of existing methods, through an extensive three-part validation study...
  • NETAL

  • Referenced in 3 articles [sw34152]
  • uses a greedy method, based on the alignment scoring matrix, which is derived from both ... network alignment. NETAL outperforms other global alignment methods in terms of several measurements, such...
  • LOCSVMPSI

  • Referenced in 11 articles [sw22457]
  • paper, a novel method named LOCSVMPSI has been introduced, which is based on the support ... vector machine (SVM) and the position-specific scoring matrix generated from profiles of PSI-BLAST ... were consistently better than the previous method based on several SVMs using composition of both...
  • ErmineJ

  • Referenced in 4 articles [sw30047]
  • over-representation and resampling-based methods that focus on gene scores or correlation of gene...
  • DNA

  • Referenced in 5 articles [sw26923]
  • examples of this score is provided. We carried out our method on two types ... based on differential equations. We show that, for appropriate choices of the connectivity scores ... tuning parameters, our method works well on simulated data. We also analyze a real data...
  • TERA

  • Referenced in 3 articles [sw34318]
  • species tree aware method for gene tree reconstruction based on a scoring scheme combining duplication ... corresponding probabilistic method while being faster, and outperforms other parsimony-based methods in both accuracy...
  • COMPASS

  • Referenced in 9 articles [sw23109]
  • with assessment of statistical significance (COMPASS). The method derives numerical profiles from alignments, constructs optimal ... detected similarities. The scoring system and E-value calculation are based on a generalization ... profile-profile case. Tested along with existing methods for profile-sequence (PSI-BLAST) and profile...
  • brglm2

  • Referenced in 8 articles [sw19510]
  • linear models based on various methods for bias reduction. The brglmFit fitting method can achieve ... estimation bias either through the adjusted score equations approach in Firth (1993) <
  • IsoRankN

  • Referenced in 10 articles [sw08325]
  • induced graph of pairwise alignment scores. IsoRankN outperforms existing algorithms for global network alignment ... five available eukaryotic networks. Being based on spectral methods, IsoRankN is both error-tolerant...
  • GRAPPA

  • Referenced in 11 articles [sw17255]
  • include distance-based methods, parsimony methods using sequence-based encodings, and direct optimization. The latter ... genomes because the running time of its scoring algorithm grows exponentially with the number ... genome. We report here on a new method to compute a tight lower bound...
  • ccdrAlgorithm

  • Referenced in 0 articles [sw16299]
  • www.jmlr.org/papers/v16/aragam15a.html>. This is a fast, score-based method for learning Bayesian networks that uses...
  • HapCUT

  • Referenced in 6 articles [sw35352]
  • combinatorial approach for the haplotype assembly problem based on computing max-cuts in certain graphs ... this individual. We have applied our method HapCUTto infer haplotypes from this data and demonstrate ... correction scores for all chromosomes) than the greedy heuristic and a previously published method, Fast ... Hare. We also describe a maximum likelihood based estimator of the absolute accuracy...
  • CONTRAfold

  • Referenced in 8 articles [sw17117]
  • novel secondary structure prediction method based on conditional log-linear models (CLLMs), a flexible class ... using discriminative training and feature-rich scoring. By incorporating most of the features found...
  • ProbCons

  • Referenced in 14 articles [sw12014]
  • paper, we introduce probabilistic consistency, a novel scoring function for multiple sequence comparisons. We present ... tool for progressive protein multiple sequence alignment based on probabilistic consistency, and evaluate its performance ... achieves statistically significant improvement over other leading methods while maintaining practical speed. ProbCons is publicly...
  • DeepSleepNet

  • Referenced in 2 articles [sw21053]
  • named DeepSleepNet, for automatic sleep stage scoring based on raw single-channel ... effectively train such model. Methods: Most of the existing methods rely on hand-engineered features ... which require prior knowledge about sleep stage scoring. Only a few of them encode...
  • SKAT

  • Referenced in 3 articles [sw26433]
  • regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual ... score statistics in a SNP set and efficiently compute SNP-set level p-values...