• MUSCLE

  • Referenced in 71 articles [sw13193]
  • Muscle: multiple sequence alignment with high accuracy and high throughput. We describe MUSCLE ... fast distance estimation using kmer counting, progressive alignment using a new profile function we call ... tree‐dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T‐Coffee ... CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark...
  • Kalign

  • Referenced in 13 articles [sw13194]
  • Kalign, while maintaining its high alignment accuracy. Kalign version 2 also supports nucleotide alignment ... efficient, permitting accurate alignment of very large numbers of sequences. The accuracy of Kalign2 compares ... case of protein alignments while its accuracy on nucleotide alignments is generally superior. In addition ... predicted sequence annotation to improve the alignment accuracy. Kalign2 is freely available for download from...
  • RAPTOR

  • Referenced in 19 articles [sw09002]
  • terms of the recognition capability and alignment accuracy for Fold Recognition (FR) family targets. RAPTOR...
  • T-coffee

  • Referenced in 39 articles [sw13195]
  • multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice ... popular progressive approach to multiple alignment but avoids the most serious pitfalls caused...
  • OXBench

  • Referenced in 5 articles [sw22988]
  • evaluation of protein multiple sequence alignment accuracy. BACKGROUND: The alignment of two or more protein ... current state-of-the art for alignment accuracy and provides a baseline against which ... majority of the improvement in alignment accuracy seen since 1985 stems from improved pair-score ... than algorithmic refinements. The maximum theoretical alignment accuracy obtained by pooling results over all methods...
  • FUGUE

  • Referenced in 9 articles [sw16894]
  • improves both homology recognition performance and alignment accuracy...
  • LAGAN

  • Referenced in 17 articles [sw13192]
  • several megabases can be aligned in minutes) with high accuracy. The results of the alignment...
  • Probalign

  • Referenced in 6 articles [sw24613]
  • MOTIVATION: The maximum expected accuracy optimization criterion for multiple sequence alignment uses pairwise posterior probabilities ... residues to align sequences. The partition function methodology is one way of estimating these probabilities ... first time to construct maximal expected accuracy sequence alignments. RESULTS: We bridge the two techniques ... length datasets containing protein repeats. Here, alignment accuracy scores are at least...
  • TM-align

  • Referenced in 14 articles [sw22248]
  • average, the resulting structure alignments have higher accuracy and coverage than those provided by these...
  • CONTRAlign

  • Referenced in 4 articles [sw08305]
  • example alignments, CONTRAlign achieves alignment accuracies competitive with available modern tools. As confirmed by rigorous ... effectively leverages weak biological signals in sequence alignment: using CONTRAlign, we find that hydropathy-based ... improvements of 5-6% in aligner accuracy for sequences with less than 20% identity ... alignment accuracy for low-identity sequences...
  • 3DCoffee

  • Referenced in 6 articles [sw12008]
  • HOMSTRAD, the collection of reference structural alignments. We found that combining TCoffee with the threading ... Fugue makes it possible to improve the accuracy of our HOMSTRAD dataset by four percentage ... linear correlation between multiple sequence alignment accuracy and the ratio of number of provided structure ... enough for computing an accurate multiple sequence alignment...
  • RAxML

  • Referenced in 34 articles [sw07716]
  • sequential speed and accuracy of RAxML and PHYML on 8 synthetic alignments comprising 4.000 sequences...
  • BFAST

  • Referenced in 4 articles [sw20962]
  • importance, but equally important is maintaining alignment accuracy of short reads ... freely available implementation, BFAST, which can align data produced by any of current sequencing platforms ... user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient ... alignment tools - BLAT, MAQ, SHRiMP, and SOAP - in terms of both speed and accuracy, using...
  • PROMALS

  • Referenced in 4 articles [sw22476]
  • predictions from PSIPRED. PROMALS shows higher alignment accuracy than other advanced methods, such as MUMMALS ... input. The output includes a colored alignment augmented with information about sequence grouping, predicted secondary...
  • MSAProbs

  • Referenced in 3 articles [sw12007]
  • profile alignment, are incorporated to improve alignment accuracy. Assessed using the popular benchmarks: BAliBASE, PREFAB ... achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE...
  • MICAlign

  • Referenced in 2 articles [sw12010]
  • were automatically learned. MICAlign showed improved alignment accuracy over several other state...
  • Facet

  • Referenced in 1 article [sw24607]
  • accuracy estimation of protein multiple sequence alignments. The accuracy of a protein multiple sequence alignment ... accuracy of a computed alignment. A good accuracy estimator has broad utility, from building ... collection of aligners (see Ensemble Alignment), to boosting the accuracy of a single aligner ... Local Realignment). To estimate accuracy of a computed multiple sequence alignment we have developed Facet...
  • MAMMOTH

  • Referenced in 11 articles [sw26215]
  • describe random structural alignments of proteins with different folds with good accuracy by an extreme ... likelihood of obtaining a given structural alignment by chance. The performance of the derived score...
  • MUMMALS

  • Referenced in 4 articles [sw13110]
  • homologs, MUMMALS achieves statistically best accuracy among several leading aligners, such as ProbCons, MAFFT...
  • Expresso

  • Referenced in 2 articles [sw12009]
  • information is available, Expresso delivers sequence alignments with accuracy comparable with structure-based alignments...