• ClustalW

  • Referenced in 129 articles [sw12016]
  • improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties...
  • MUSCLE

  • Referenced in 70 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 on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark ... tested methods for large numbers of sequences, aligning 5000 sequences of average length...
  • T-coffee

  • Referenced in 39 articles [sw13195]
  • method for fast and accurate multiple sequence alignment. We describe a new method (T-Coffee ... multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice ... pair-wise alignments between the sequences. This provides us with a library of alignment information ... also on how all of the sequences align with each other. This alignment information...
  • BLAST

  • Referenced in 232 articles [sw17334]
  • Basic Local Alignment Search Tool. BLAST finds regions of similarity between biological sequences. The program...
  • MUMMER

  • Referenced in 39 articles [sw17256]
  • MUMmer Ultra-fast alignment of large-scale DNA and protein sequences. MUMmer is a system ... contigs from a shotgun sequencing project, and will align them to another set of contigs ... divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate ... alignments based upon the six-frame translations of both input sequences. The original MUMmer system...
  • DIALIGN

  • Referenced in 32 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 ... therefore be applied to sequence data that cannot be correctly aligned by more traditional approaches...
  • MAFFT

  • Referenced in 31 articles [sw08304]
  • nucleotide sequences. MAFFT is a multiple sequence alignment program for unix-like operating systems ... accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment...
  • WebLogo

  • Referenced in 24 articles [sw17263]
  • patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description ... than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult ... stack for each position in the sequence. The overall height of each stack indicates...
  • Chimera

  • Referenced in 34 articles [sw10908]
  • data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High...
  • Rfam

  • Referenced in 32 articles [sw04637]
  • families, each represented by multiple sequence alignments, consensus secondary structures and covariance models ... better preserved than the RNA sequence. The CMs used to describe each family...
  • BIONJ

  • Referenced in 29 articles [sw08301]
  • algorithm based on a simple model of sequence data. We propose an improved version ... when these estimates are obtained from aligned sequences. At each step it permits the selection...
  • Clustal X

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

  • Referenced in 25 articles [sw09655]
  • only a careful examination of the sequence alignments that focused on the conserved residues provided ... that the high scores were fortuitous. As sequence comparison methods become more powerful by becoming...
  • MODELLER

  • Referenced in 32 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...
  • ProbCons

  • Referenced in 14 articles [sw12014]
  • ProbCons: probabilistic consistency-based multiple sequence alignment. To study gene evolution across a wide range ... biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments, however ... lack of proper objective functions for measuring alignment quality. In this paper, we introduce probabilistic ... practical tool for progressive protein multiple sequence alignment based on probabilistic consistency, and evaluate...
  • Bowtie 2

  • Referenced in 20 articles [sw29190]
  • ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences...
  • 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 ... 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...
  • PISCES

  • Referenced in 25 articles [sw16873]
  • user. The sequence identities are obtained from PSI-BLAST alignments with position-specific substitution matrices ... sequence identity and often overestimates sequence identity by aligning only well-conserved fragments. PDB sequences...
  • HMMER

  • Referenced in 17 articles [sw10514]
  • single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database...
  • BLAT

  • Referenced in 34 articles [sw16891]
  • protein alignments at sensitivity settings typically used when comparing vertebrate sequences. BLAT’s speed stems ... homologous to the query sequence. It performs an alignment between homologous regions. It stitches together...