• MUSCLE

  • Referenced in 71 articles [sw13193]
  • CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark ... MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets ... tested methods for large numbers of sequences, aligning 5000 sequences of average length...
  • RAPTOR

  • Referenced in 19 articles [sw09002]
  • test by the protein structure prediction community, ranks RAPTOR as top 1, among individual prediction ... terms of the recognition capability and alignment accuracy for Fold Recognition (FR) family targets. RAPTOR...
  • ARTool

  • Referenced in 0 articles [sw17414]
  • package ARTool. Aligned Rank Transform. The Aligned Rank Transform for nonparametric factorial ANOVAs as described ... Gergle, & J. J. Higgins, ”The Aligned Rank Transform for nonparametric factorial analyses using only ANOVA...
  • Probalign

  • Referenced in 6 articles [sw24613]
  • MUSCLE) on the BAliBASE 3.0 protein alignment benchmark. Similarly, Probalign also outperforms these methods ... HOMSTRAD and OXBENCH benchmarks. Probalign ranks statistically highest (P-value < 0.005) on all three benchmarks ... data. Finally, our method also produces accurate alignments on long and heterogeneous length datasets containing...
  • IOTA

  • Referenced in 7 articles [sw19593]
  • TOCSY - Toolboxes for Complex Systems: Inner composition alignment (IOTA) is a permutation-based association measure ... series is reodered with regards to the rank order of a second...
  • Meteor

  • Referenced in 4 articles [sw33894]
  • metric scores are calculated based on the alignments between hypothesis-reference pairs. The metric includes ... emulate various human judgment tasks including WMT ranking and NIST adequacy. The current version also...
  • CVTree3

  • Referenced in 7 articles [sw22015]
  • latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3 ... order with prokaryotic classification at all taxonomic ranks from domains down to species and strains...
  • PathBLAST

  • Referenced in 7 articles [sw29737]
  • basic method searches for high-scoring alignments between pairs of protein interaction paths, for which ... from a network database. PathBLAST returns a ranked list of matching paths from the target...
  • CompaRNA

  • Referenced in 2 articles [sw16474]
  • best single-sequence methods if an alignment of homologous RNA sequences is available. This article ... October 2012, whereas the rankings presented online are continuously updated. We will gladly include...
  • Hmmpfam

  • Referenced in 1 article [sw01294]
  • location.The output consists of three sections: a ranked list of the best scoring HMMs ... their occurrence in the sequence, and alignments for all the best scoring domains. A sequence...
  • ATLAS

  • Referenced in 197 articles [sw00056]
  • This paper describes the Automatically Tuned Linear Algebra...
  • CGAL

  • Referenced in 355 articles [sw00118]
  • The goal of the CGAL Open Source Project...
  • Coq

  • Referenced in 1784 articles [sw00161]
  • Coq is a formal proof management system. It...
  • CSDP

  • Referenced in 197 articles [sw00169]
  • CSDP, A C Library for Semidefinite Programming. This...
  • Gmsh

  • Referenced in 576 articles [sw00366]
  • Gmsh is a 3D finite element grid generator...
  • LEDA

  • Referenced in 261 articles [sw00509]
  • In the core computer science areas -- data structures...
  • MapReduce

  • Referenced in 250 articles [sw00546]
  • MapReduce is a new parallel programming model initially...
  • Mathematica

  • Referenced in 5883 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 12074 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • polymake

  • Referenced in 292 articles [sw00724]
  • polymake is open source software for research in...