• PROMALS

  • Referenced in 5 articles [sw22476]
  • server for accurate multiple protein sequence alignments. Multiple sequence alignments are essential in homology inference ... server that constructs multiple protein sequence alignments using PROMALS, a progressive method that improves alignment...
  • MAVG

  • Referenced in 9 articles [sw10918]
  • genomic sequence, and annotating multiple sequence alignments. Availability: http://iubio.bio.indiana.edu/soft/molbio/pattern/cpg_islands/...
  • DIALIGN-TX

  • Referenced in 7 articles [sw12751]
  • progressive approaches for segment-based multiple sequence alignment. Background: DIALIGN-T is a reimplementation ... multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments ... locally and globally related sequence sets than previous versions of DIALIGN. However, like the original ... greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy approaches...
  • Kalign

  • Referenced in 14 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 ... maintaining its high alignment accuracy. Kalign version 2 also supports nucleotide alignment, and a newly ... introduced extension allows for external sequence annotation to be included into the alignment procedure...
  • PCMA

  • Referenced in 4 articles [sw24612]
  • PCMA: fast and accurate multiple sequence alignment based on profile consistency. PCMA (profile consistency multiple ... sequence alignment) is a progressive multiple sequence alignment program that combines two different alignment strategies...
  • Noisy

  • Referenced in 5 articles [sw21022]
  • Noisy: identification of problematic columns in multiple sequence alignments. MOTIVATION: Sequence-based methods for phylogenetic ... rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern ... randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals ... phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears...
  • PSICOV

  • Referenced in 5 articles [sw17010]
  • sparse inverse covariance estimation on large multiple sequence alignments. Motivation: The accurate prediction of residue ... rapid growth in the sizes of sequence families. Progress could have major impacts in both ... made by identifying correlated mutations within multiple sequence alignments (MSAs), most commonly through the information...
  • OXBench

  • Referenced in 7 articles [sw22988]
  • benchmark for evaluation of protein multiple sequence alignment accuracy. BACKGROUND: The alignment ... alignment. In this paper we describe a suite of reference alignments derived from the comparison ... generated alignments to be benchmarked. We test the OXBench benchmark suite on alignments generated ... judged. RESULTS: The simple hierarchical multiple alignment algorithm, AMPS, performed as well as or better...
  • INDELible

  • Referenced in 7 articles [sw23043]
  • many inference methods, including those for multiple sequence alignment, phylogenetic tree inference, and ancestral sequence...
  • M-Coffee

  • Referenced in 4 articles [sw22982]
  • Coffee: combining multiple sequence alignment methods with T-Coffee. We introduce M-Coffee, a meta ... method for assembling multiple sequence alignments (MSA) by combining the output of several individual methods...
  • MUMMALS

  • Referenced in 4 articles [sw13110]
  • MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information ... have developed MUMMALS, a program to construct multiple ... protein sequence alignment using probabilistic consistency. MUMMALS improves alignment quality by using pairwise alignment hidden ... alignment parameters and performance tests; (iii) reference-independent evaluation of alignment quality using sequence alignment...
  • MSAProbs

  • Referenced in 3 articles [sw12007]
  • MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities ... Motivation: Multiple sequence alignment is of central importance to bioinformatics and computational biology. Although ... number of algorithms for computing a multiple sequence alignment have been designed, the efficient computation ... practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based...
  • Mauve

  • Referenced in 16 articles [sw24606]
  • Mauve: multiple alignment of conserved genomic sequence with rearrangements. As genomes evolve, they undergo large...
  • PROMALS3D

  • Referenced in 3 articles [sw16918]
  • PROMALS3D: Multiple Protein Sequence Alignment Enhanced with ... Evolutionary and Three-Dimensional Structural Information. Multiple sequence alignment (MSA) is an essential tool with ... combines them with sequence-based constraints of profile–profile alignments in a consistency ... based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment...
  • RASCAL

  • Referenced in 3 articles [sw24615]
  • RASCAL: rapid scanning and correction of multiple sequence alignments. MOTIVATION: Most multiple sequence alignment programs...
  • NAST

  • Referenced in 3 articles [sw13835]
  • NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Microbiologists conducting ... bacterial and archaeal diversity often require comparative alignments of thousands of 16S rRNA genes collected ... bioinformatics expertise required to construct such an alignment has inhibited high-throughput analysis ... Alignment Space Termination) algorithm for creating multiple sequence alignments (MSA). The tool was implemented with...
  • MergeAlign

  • Referenced in 2 articles [sw24604]
  • program that constructs a consensus multiple sequence alignment from multiple independent alignments. Using dynamic programming ... efficiently combines individual multiple sequence alignments to generate a consensus that is maximally representative ... constituent alignments. Using MergeAlign to combine multiple sequence alignments generated using different matrices of amino ... acid substitution produces multiple sequence alignments that are more robust and more accurate than alignments...
  • MuSiC

  • Referenced in 3 articles [sw35658]
  • MuSiC: a tool for multiple sequence alignment with constraints. MuSiC is a web server ... such that the user-specified residues/nucleotides are aligned with each other. The input ... system consists of a set of protein/DNA/RNA sequences and a set of user-specified constraints ... output of MuSiC is a constrained multiple sequence alignment in which the fragments...
  • JPred

  • Referenced in 7 articles [sw35977]
  • server allows a single sequence or multiple alignment to be submitted, and returns predictions from ... algorithms that exploit evolutionary information from multiple sequences. A consensus prediction is also returned which...
  • AQUA

  • Referenced in 2 articles [sw24611]
  • AQUA: automated quality improvement for multiple sequence alignments. Multiple sequence alignment (MSA) is a central ... AQUA for ’Automated quality improvement for multiple sequence alignments’. Our current implementation relies...