• CLUSTAL

  • Referenced in 17 articles [sw12750]
  • performing multiple alignments of large numbers of amino acid or nucleotide sequences is described ... pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. Then the multiple alignment ... from a series of pairwise alignments of clusters of sequences, following the order of branching...
  • 3DCoffee

  • Referenced in 6 articles [sw12008]
  • uses a mixture of pairwise sequence alignments and pairwise structure comparison methods to generate multiple...
  • Probalign

  • Referenced in 6 articles [sw24613]
  • accuracy optimization criterion for multiple sequence alignment uses pairwise posterior probabilities of residues to align...
  • CONTRAlign

  • Referenced in 4 articles [sw08305]
  • Contralign: discriminative training for protein sequence alignment. In this paper, we present CONTRAlign, an extensible ... framework for parameter learning and protein pairwise sequence alignment using pair conditional random fields. When...
  • DIALIGN-TX

  • Referenced in 7 articles [sw12751]
  • better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However ... greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy approaches ... previous greedy algorithm with a progressive alignment approach...
  • GapsMis

  • Referenced in 1 article [sw11923]
  • with a bounded number of gaps. Pairwise sequence alignment techniques have gained renewed interest ... present GapsMis, an algorithm for pairwise global sequence alignment with a variable, but bounded, number ... analogous algorithm for pairwise local sequence alignment with a variable, but bounded, number of gaps ... GapsMis-L we performed millions of pairwise sequence alignments under realistic conditions, based...
  • parasail

  • Referenced in 1 article [sw28779]
  • parasail: Pairwise Sequence Alignment Library. parasail is a SIMD C (C99) library containing implementations ... Wunsch (global), and various semi-global pairwise sequence alignment algorithms. Here, semi-global means insertions ... implements most known algorithms for vectorized pairwise sequence alignment, including diagonal [Wozniak, 1997], blocked [Rognes...
  • R-Coffee

  • Referenced in 2 articles [sw17130]
  • Coffee to compute multiple sequence alignments combining the pairwise output of sequence aligners and structural ... suggest that the best protocol for aligning short sequences (less than ... Coffee with the RNA pairwise structural aligner Consan. We also show that the simultaneous combination ... four best sequence alignment programs with R-Coffee produces alignments almost as accurate as those...
  • CentroidAlign

  • Referenced in 2 articles [sw17119]
  • fast predictions of multiple alignments for RNA sequences has increased due to recent findings about ... designed a novel estimator for multiple alignments of structured RNAs, based on maximizing the expected ... expected accuracy (MEA) estimator for pairwise alignment of RNA sequences. This maximizes the expected ... secondary structures and all the pairwise alignments as input sequences. Moreover, we integrate the probabilistic...
  • NextGenMap

  • Referenced in 1 article [sw23012]
  • have to be evaluated by a pairwise sequence alignment. Moreover, NextGenMap uses fast SIMD instructions...
  • PanCake

  • Referenced in 1 article [sw08336]
  • which are derived from genome-wide pairwise sequence alignments. We discuss the design...
  • JAligner

  • Referenced in 1 article [sw21461]
  • Gotoh’s improvement for biological local pairwise sequence alignment using the affine gap penalty model...
  • FPQRNA

  • Referenced in 1 article [sw18995]
  • Phenom 9650 Quad CPU for pairwise sequence alignment with 996 residues, however the power consumption...
  • MARNA

  • Referenced in 5 articles [sw35539]
  • sequence structure comparisons. Results: We describe a novel approach for multiple alignment of RNAs (MARNA ... based on pairwise sequence–structure comparisons of RNAs. From these sequence–structure alignments, libraries...
  • MISHIMA

  • Referenced in 2 articles [sw35227]
  • multiple sequence alignment methods. Conventional multiple alignment methods are based on pairwise alignment and/or progressive ... have performance problems when the number of sequences is large and when dealing with genome ... terms of Multiple Alignment), that does not depend on pairwise sequence comparison. A new algorithm ... sequences. Divide and conquer approach is then applied to break the sequences into fragments that...
  • PairProSVM

  • Referenced in 5 articles [sw35332]
  • Protein Subcellular Localization Based on Local Pairwise Profile Alignment and SVM. The subcellular locations ... sequences in the training set are constructed by PSI-BLAST, and the pairwise profile alignment ... outperforms the methods that are based on sequence alignment and amino acid compositions even...
  • MUMMALS

  • Referenced in 4 articles [sw13110]
  • protein sequence alignment using probabilistic consistency. MUMMALS improves alignment quality by using pairwise alignment hidden ... collection (>10 000) of automatically computed pairwise structure alignments of divergent protein domains is superior ... alignment parameters and performance tests; (iii) reference-independent evaluation of alignment quality using sequence alignment...
  • HHpred

  • Referenced in 7 articles [sw17271]
  • prediction and is the first to implement pairwise comparison of profile hidden Markov models (HMMs ... accepts a single query sequence or a multiple alignment as input. Within only ... similarity. HHpred can produce pairwise query-template alignments, multiple alignments of the query with ... alignments. A detailed help facility is available. As a demonstration, we analyze the sequence...
  • ddbRNA

  • Referenced in 1 article [sw35749]
  • detection of conserved secondary structures in multiple alignments. Motivation: Structured non-coding RNAs (ncRNAs) have ... secondary structures in both pairwise and multiple DNA sequence alignments with computational time proportional ... sequence length. We implemented the algorithm for the case of pairwise and three-way alignments...
  • Minimap2

  • Referenced in 1 article [sw28780]
  • Minimap2: pairwise alignment for nucleotide sequences. Recent advances in sequencing technologies promise ultra-long reads...