• ClustalW

  • Referenced in 133 articles [sw12016]
  • improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties...
  • 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...
  • 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 ... pair-wise alignments between the sequences. This provides us with a library of alignment information...
  • MAFFT

  • Referenced in 41 articles [sw08304]
  • nucleotide sequences. MAFFT is a multiple sequence alignment program for unix-like operating systems ... multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences...
  • Rfam

  • Referenced in 33 articles [sw04637]
  • families, each represented by multiple sequence alignments, consensus secondary structures and covariance models...
  • Clustal X

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

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

  • Referenced in 17 articles [sw12750]
  • CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. An approach for performing ... multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method ... multiple alignment is achieved from a series of pairwise alignments of clusters of sequences, following...
  • 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...
  • MODELLER

  • Referenced in 33 articles [sw27731]
  • user provides an alignment of a sequence to be modeled with known related structures ... flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence...
  • CAP3

  • Referenced in 16 articles [sw08935]
  • overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences...
  • 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...
  • 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...
  • 3DCoffee

  • Referenced in 6 articles [sw12008]
  • combining protein sequences and structures within multiple sequence alignments. Most bioinformatics analyses require the assembly ... multiple sequence alignment. It has long been suspected that structural information can help to improve ... order to generate high-quality multiple sequence alignments. 3DCoffee is based on TCoffee version ... pairwise structure comparison methods to generate multiple sequence alignments. We benchmarked 3DCoffee using a subset...
  • Rose

  • Referenced in 8 articles [sw16613]
  • history is logged and the `correct’ multiple sequence alignment is created simultaneously. The model also ... mutation within the sequences, making it possible to establish so-called sequence motifs. The data ... evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships...
  • HMMER

  • Referenced in 17 articles [sw10514]
  • either a single protein sequence, multiple protein sequence alignment or profile HMM against a target ... user expertise and accepts batch uploading of multiple queries at once. All search methods...
  • Probalign

  • Referenced in 6 articles [sw24613]
  • Probalign: multiple sequence alignment using partition function posterior probabilities. MOTIVATION: The maximum expected accuracy optimization ... criterion for multiple sequence alignment uses pairwise posterior probabilities of residues to align sequences ... time to construct maximal expected accuracy sequence alignments. RESULTS: We bridge the two techniques within ... generally more accurate than other leading multiple sequence alignment methods (i.e. Probcons, MAFFT and MUSCLE...
  • FUGUE

  • Referenced in 9 articles [sw16894]
  • uses the global-local algorithm to align a sequence-structure pair when they greatly differ ... SSEs. (3) Combined information from both multiple sequences ... multiple structures. FUGUE is designed to align multiple sequences against multiple structures to enrich ... FUGUE improves both homology recognition performance and alignment accuracy...