• MUSCLE

  • Referenced in 71 articles [sw13193]
  • Muscle: multiple sequence alignment with high accuracy and high throughput. We describe MUSCLE ... computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast...
  • ClustalW

  • Referenced in 133 articles [sw12016]
  • improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties...
  • MAFFT

  • Referenced in 41 articles [sw08304]
  • MAFFT: Multiple alignment program for amino acid or nucleotide sequences. MAFFT is a multiple sequence ... systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment...
  • T-coffee

  • Referenced in 39 articles [sw13195]
  • novel method for fast and accurate multiple sequence alignment. We describe a new method ... Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest ... popular progressive approach to multiple alignment but avoids the most serious pitfalls caused...
  • MODELLER

  • Referenced in 33 articles [sw27731]
  • structures (1,2). The user provides an alignment of a sequence to be modeled with ... flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence...
  • Balibase

  • Referenced in 28 articles [sw08913]
  • alignment database for the evaluation of multiple alignment programs...
  • CLUSTAL

  • Referenced in 17 articles [sw12750]
  • CLUSTAL: a package for performing multiple sequence alignment ... microcomputer. An approach for performing multiple alignments of large numbers of amino acid or nucleotide ... fast pairwise alignment algorithm. Then the multiple alignment is achieved from a series of pairwise...
  • DIALIGN

  • Referenced in 33 articles [sw12015]
  • DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. DIALIGN is a widely used software ... tool for multiple DNA and protein sequence alignment. The program combines local and global alignment...
  • Rfam

  • Referenced in 32 articles [sw04637]
  • families, each represented by multiple sequence alignments, consensus secondary structures and covariance models...
  • LAGAN

  • Referenced in 17 articles [sw13192]
  • pairwise aligner (LAGAN), a multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN...
  • Kalign

  • Referenced in 13 articles [sw13194]
  • Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features ... growing field of genomics, multiple alignment programs are confronted with ever increasing amounts of data...
  • ProbCons

  • Referenced in 14 articles [sw12014]
  • ProbCons: probabilistic consistency-based multiple sequence alignment. To study gene evolution across a wide range ... organisms, biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments ... alignment quality. In this paper, we introduce probabilistic consistency, a novel scoring function for multiple ... practical tool for progressive protein multiple sequence alignment based on probabilistic consistency, and evaluate...
  • Clustal X

  • Referenced in 28 articles [sw16249]
  • Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten...
  • Jalview

  • Referenced in 10 articles [sw22983]
  • Jalview Java alignment editor. Multiple sequence alignment remains a crucial method for understanding the function ... However, it is known that automatic multiple sequence alignments can often be improved by manual ... needed to view and edit multiple sequence alignments. Due to growth in the sequence databases ... multiple sequence alignments can often be large and difficult to view efficiently. The Jalview Java...
  • WebLogo

  • Referenced in 24 articles [sw17263]
  • representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer...
  • IsoRankN

  • Referenced in 10 articles [sw08325]
  • describe IsoRankN (IsoRank-Nibble), a global multiple-network alignment tool based on spectral clustering ... alignment in coverage and consistency on multiple alignments of the five available eukaryotic networks. Being...
  • SEGID

  • Referenced in 9 articles [sw35743]
  • SEGID: Identifying Interesting Segments in (Multiple) Sequence Alignments. Summary: SEGID is a tool for finding ... high scores) for a given (multiple) sequence alignment. It takes a (multiple) sequence alignment...
  • HHpred

  • Referenced in 7 articles [sw17271]
  • single query sequence or a multiple alignment as input. Within only a few minutes ... HHpred can produce pairwise query-template alignments, multiple alignments of the query with...
  • Infernal

  • Referenced in 11 articles [sw17000]
  • covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal uses ... databases and to create potentially large multiple sequence alignments. Version 1.1 of Infernal introduces...
  • Mauve

  • Referenced in 11 articles [sw24606]
  • Mauve: multiple alignment of conserved genomic sequence with rearrangements. As genomes evolve, they undergo large...