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Recent Evolutions of Multiple Sequence Alignment Algorithms
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1006/jmbi.2000.4042openalex-snapshot
T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1006/jmbi.2001.4762openalex-snapshot
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties11Edited by B. Honig
inferredcites →https://doi.org/10.1007/11557067_25openalex-snapshot
Multiple Structural RNA Alignment with Lagrangian Relaxation
inferredcites →https://doi.org/10.1007/bf02257378openalex-snapshot
The alignment of sets of sequences and the construction of phyletic trees: An integrated method
inferredcites →https://doi.org/10.1016/0022-2836(86)90308-6openalex-snapshot
Identification of protein sequence homology by consensus template alignment
inferredcites →https://doi.org/10.1016/0022-2836(89)90084-3openalex-snapshot
Protein structure alignment
inferredcites →https://doi.org/10.1016/j.jmb.2004.04.058openalex-snapshot
3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments
inferredcites →https://doi.org/10.1016/j.sbi.2005.04.002openalex-snapshot
Multiple sequence alignments
inferredcites →https://doi.org/10.1016/j.sbi.2006.04.004openalex-snapshot
Multiple sequence alignment
inferredcites →https://doi.org/10.1016/s0065-227x(99)80007-0openalex-snapshot
Multiple sequence alignment: Algorithms and applications
inferredcites →https://doi.org/10.1073/pnas.93.22.12098openalex-snapshot
Multiple DNA and protein sequence alignment based on segment-to-segment comparison.
inferredcites →https://doi.org/10.1093/bioinformatics/18.9.1243openalex-snapshot
The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs
inferredcites →https://doi.org/10.1093/bioinformatics/btg008openalex-snapshot
PCMA: fast and accurate multiple sequence alignment based on profile consistency
inferredcites →https://doi.org/10.1093/bioinformatics/btg1029openalex-snapshot
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments
inferredcites →https://doi.org/10.1093/bioinformatics/bti582openalex-snapshot
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures
inferredcites →https://doi.org/10.1093/bioinformatics/btl218openalex-snapshot
The iRMSD: a local measure of sequence alignment accuracy using structural information
inferredcites →https://doi.org/10.1093/bioinformatics/btm017openalex-snapshot
PROMALS: towards accurate multiple sequence alignments of distantly related proteins
inferredcites →https://doi.org/10.1093/nar/22.22.4673openalex-snapshot
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
inferredcites →https://doi.org/10.1093/nar/28.15.2919openalex-snapshot
DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches
inferredcites →https://doi.org/10.1093/nar/gkh400openalex-snapshot
CaspR: a web server for automated molecular replacement using homology modelling
inferredcites →https://doi.org/10.1093/nar/gki1020openalex-snapshot
Automatic assessment of alignment quality
inferredcites →https://doi.org/10.1093/nar/gki198openalex-snapshot
MAFFT version 5: improvement in accuracy of multiple sequence alignment
inferredcites →https://doi.org/10.1093/nar/gki390openalex-snapshot
PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information
inferredcites →https://doi.org/10.1093/nar/gkl091openalex-snapshot
M-Coffee: combining multiple sequence alignment methods with T-Coffee
inferredcites →https://doi.org/10.1093/nar/gkl092openalex-snapshot
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee
inferredcites →https://doi.org/10.1093/nar/gkl191openalex-snapshot
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment
inferredcites →https://doi.org/10.1093/nar/gkl514openalex-snapshot
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information
inferredcites →https://doi.org/10.1093/protein/13.11.745openalex-snapshot
ProSup: a refined tool for protein structure alignment
inferredcites →https://doi.org/10.1101/gr.2821705openalex-snapshot
ProbCons: Probabilistic consistency-based multiple sequence alignment
inferredcites →https://doi.org/10.1110/ps.8.3.654openalex-snapshot
Protein structure comparison using iterated double dynamic programming
inferredcites →https://doi.org/10.1186/1471-2105-5-113openalex-snapshot
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
inferredcites →https://doi.org/10.1186/1471-2105-6-298openalex-snapshot
Kalign – an accurate and fast multiple sequence alignment algorithm
inferredcites →https://doi.org/10.3233/isb-00245openalex-snapshot
Analysis and Comparison of Benchmarks for Multiple Sequence Alignment
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Sequence Homology Handling
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PROMALS3D: Multiple Protein Sequence Alignment Enhanced with Evolutionary and Three-Dimensional Structural Information
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T-Coffee: Tree-Based Consistency Objective Function for Alignment Evaluation
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Sequence Comparison: Theory and Methods
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Serious Games for Solving Protein Sequence Alignments - Combining Citizen Science and Gaming
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RRCA: Ultra-Fast Multiple In-species Genome Alignments
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Efficient and Effective Multiple Protein Sequence Alignment Model Using Dynamic Progressive Approach with Novel Look Back Ahead Scoring System
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Homology Search and Multiple Alignment
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A Similarity Measure for Sequences of Categorical Data Based on the Ordering of Common Elements
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Information Content of Sets of Biological Sequences Revisited
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Co-evolution and Information Signals in Biological Sequences
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A Tiling Bound for Pairwise Global Sequence Alignment
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A Novel Method for Progressive Multiple Sequence Alignment Based on Lempel-Ziv
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Alignment of Protein Sequences
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A Parallel Niched Pareto Evolutionary Algorithm for Multiple Sequence Alignment
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PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling
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2D Shapes Classification Using BLAST
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Comparative Protein Structure Modelling
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Proposed Better Sequence Alignment for Identification of Organisms Using DNA Barcode
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Multiple Sequence Alignment Algorithm Using Adaptive Evolutionary Clustering
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Similarity clustering of proteins using substantive knowledge and reconstruction of evolutionary gene histories in herpesvirus
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A comprehensive systematic literature review of multiple sequence alignment algorithms
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Improving multiple sequence alignment biological accuracy through genetic algorithms
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Identification of gene variant associated with Parkinson’s disease using genomic databases
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DNA^+Pro^: an Improved Progressive Multiple Sequence Alignment Algorithm for Evolutionary Analysis Using Combined DNA-Protein Sequences
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Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA)
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Inferring phylogenies of evolving sequences without multiple sequence alignment
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Molecular homology and multiple-sequence alignment: an analysis of concepts and practice
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Sequence context-specific profiles for homology searching
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Evolutionary Principles Applied to Disease Control and Health Management in Shrimp Aquaculture
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Retention-error patterns in complex alphanumeric serial-recall tasks
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A novel pairwise sequence alignment algorithm for similarity search in massive datasets
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Recent developments in the MAFFT multiple sequence alignment program
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Biclustering as a method for RNA local multiple sequence alignment
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Model-based prediction of sequence alignment quality
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Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
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Jalview Version 2—a multiple sequence alignment editor and analysis workbench
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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
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Upcoming challenges for multiple sequence alignment methods in the high-throughput era
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Reproducing the manual annotation of multiple sequence alignments using a SVM classifier
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SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
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PSAR-Align: improving multiple sequence alignment using probabilistic sampling
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The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection
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REvolver: Modeling Sequence Evolution under Domain Constraints
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PROMALS3D: a tool for multiple protein sequence and structure alignments
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R-Coffee: a web server for accurately aligning noncoding RNA sequences
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PSAR: measuring multiple sequence alignment reliability by probabilistic sampling
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Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families
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The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment
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Why Would Phylogeneticists Ignore Computerized Sequence Alignment?
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Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets
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The phylogenetic placement of the non-phototrophic, Gram-positive thermophile ‘Thermobaculum terrenum’ and branching orders within the phylum ‘ Chloroflexi ’ inferred from gene order comparisons
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Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part I: Theoretical basis
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Computational Pan-Genomics: Status, Promises and Challenges
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DLPAlign: A Deep Learning based Progressive Alignment for Multiple Protein Sequences
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Cactus: Algorithms for genome multiple sequence alignment
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Alignathon: a competitive assessment of whole-genome alignment methods
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Computational intelligence in multiple sequence alignment
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Determining an Ideal MSA Method for Constructing Phylogenetic Tree on DNA Dataset
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Using protein-domain information for multiple sequence alignment
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K2: Efficient alignment-free sequence similarity measurement using the Kendall statistic
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TportHMM: Predicting the substrate class of transmembrane transport proteins using profile Hidden Markov Models
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An evolutionary approach for performing multiple sequence alignment
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Progressive Alignment and Discriminative Error Correction for Multiple OCR Engines
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Enhancing the Scalability of Consistency-based Progressive Multiple Sequences Alignment Applications
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TrioSeq: A Novel Approach to Accelerate Triplet Sequence Alignment on GPUs
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Online Log Data Analysis With Efficient Machine Learning: A Review
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Computation for Genomics Knowledge Discovery
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Parallel AlineaGA: An island parallel evolutionary algorithm for multiple sequence alignment
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From Protein Sequence to Protein Function via Multi-Label Linear Discriminant Analysis
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Trace Reconstruction Problems in Computational Biology
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Conditional Alignment Random Fields for Multiple Motion Sequence Alignment
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Historical Biogeography, Speciation, and Niche Evolution of Alouatta (Primates, Atelidae)
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Molecular Phylogenetic Analysis
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ProgSIO-MSA: Progressive-based single iterative optimization framework for multiple sequence alignment using an effective scoring system
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Finding and exploring memes in social media
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Position-Residue Specific Dynamic Gap Penalty Scoring Strategy for Multiple Sequence Alignment
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Creating Character-based Templates for Log Data to Enable Security Event Classification
inferred← citeshttps://doi.org/10.1145/3429210.3429221openalex-snapshot
DLPAlign: A Deep Learning based Progressive Alignment Method for Multiple Protein Sequences
inferred← citeshttps://doi.org/10.1146/annurev-ecolsys-110512-135822openalex-snapshot
High-Throughput Genomic Data in Systematics and Phylogenetics
inferred← citeshttps://doi.org/10.1155/2008/683509openalex-snapshot
Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods
inferred← citeshttps://doi.org/10.1155/2013/615630openalex-snapshot
An Overview of Multiple Sequence Alignments and Cloud Computing in Bioinformatics
inferred← citeshttps://doi.org/10.11606/d.41.2022.tde-09092022-145124openalex-snapshot
Caracterização dos genes que codificam proteínas que contém domínio B-BOX (BBX) em tomateiro (Solanum lycopersicum L.)
inferred← citeshttps://doi.org/10.11606/t.41.2008.tde-16092008-181652openalex-snapshot
Filogenética de Pilocarpinae (Rutaceae)
inferred← citeshttps://doi.org/10.1186/1471-2105-11-445openalex-snapshot
Automatic detection of anchor points for multiple sequence alignment
inferred← citeshttps://doi.org/10.1186/1471-2105-11-54openalex-snapshot
Towards realistic benchmarks for multiple alignments of non-coding sequences
inferred← citeshttps://doi.org/10.1186/1471-2105-14-108openalex-snapshot
LASAGNA: A novel algorithm for transcription factor binding site alignment
inferred← citeshttps://doi.org/10.1186/1471-2105-15-265openalex-snapshot
ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach
inferred← citeshttps://doi.org/10.1186/1471-2105-9-306openalex-snapshot
Grammar-based distance in progressive multiple sequence alignment
inferred← citeshttps://doi.org/10.1186/1471-2105-9-556openalex-snapshot
The meaning of alignment: lessons from structural diversity
inferred← citeshttps://doi.org/10.1186/1471-2148-10-210openalex-snapshot
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
inferred← citeshttps://doi.org/10.1186/1756-0381-3-1openalex-snapshot
A reference guide for tree analysis and visualization
inferred← citeshttps://doi.org/10.1186/1756-0500-5-340openalex-snapshot
Effect of positional dependence and alignment strategy on modeling transcription factor binding sites
inferred← citeshttps://doi.org/10.1186/gb-2010-11-4-r37openalex-snapshot
Phylogenetic assessment of alignments reveals neglected tree signal in gaps
inferred← citeshttps://doi.org/10.1186/gb-2013-14-10-r116openalex-snapshot
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment
inferred← citeshttps://doi.org/10.1186/s12859-016-0945-5openalex-snapshot
Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map
inferred← citeshttps://doi.org/10.1186/s12859-016-1105-7openalex-snapshot
General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?
inferred← citeshttps://doi.org/10.1186/s12859-016-1167-6openalex-snapshot
General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation
inferred← citeshttps://doi.org/10.1186/s12864-014-1203-8openalex-snapshot
Sampled ensemble neutrality as a feature to classify potential structured RNAs
inferred← citeshttps://doi.org/10.1186/s12920-018-0417-zopenalex-snapshot
Discovery and disentanglement of aligned residue associations from aligned pattern clusters to reveal subgroup characteristics
inferred← citeshttps://doi.org/10.12688/f1000research.10225.1openalex-snapshot
Recapitulating phylogenies using k-mers: from trees to networks
inferred← citeshttps://doi.org/10.1371/journal.pbio.1000602openalex-snapshot
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000160openalex-snapshot
The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1010665openalex-snapshot
HELIOS: High-speed sequence alignment in optics
inferred← citeshttps://doi.org/10.1371/journal.pone.0016526openalex-snapshot
Considering Transposable Element Diversification in De Novo Annotation Approaches
inferred← citeshttps://doi.org/10.1371/journal.pone.0031362openalex-snapshot
Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment
inferred← citeshttps://doi.org/10.1371/journal.pone.0069344openalex-snapshot
The Hymenopteran Tree of Life: Evidence from Protein-Coding Genes and Objectively Aligned Ribosomal Data
inferred← citeshttps://doi.org/10.1371/journal.pone.0094044openalex-snapshot
MC64-ClustalWP2: A Highly-Parallel Hybrid Strategy to Align Multiple Sequences in Many-Core Architectures
inferred← citeshttps://doi.org/10.1371/journal.pone.0110268openalex-snapshot
The Dawn of Open Access to Phylogenetic Data
inferred← citeshttps://doi.org/10.1371/journal.pone.0127431openalex-snapshot
Quantifying the Displacement of Mismatches in Multiple Sequence Alignment Benchmarks
inferred← citeshttps://doi.org/10.1371/journal.pone.0209712openalex-snapshot
Homology and linkage in crossover for linear genomes of variable length
inferred← citeshttps://doi.org/10.1515/jib-2011-174openalex-snapshot
Parallel Niche Pareto AlineaGA – an Evolutionary Multiobjective approach on Multiple Sequence Alignment
inferred← citeshttps://doi.org/10.1515/psr-2019-0098openalex-snapshot
A computer-based approach for developing linamarase inhibitory agents
inferred← citeshttps://doi.org/10.1515/sagmb-2016-0043openalex-snapshot
A time warping approach to multiple sequence alignment
inferred← citeshttps://doi.org/10.1600/036364409788606424openalex-snapshot
Utility of Secondary Structure in Phylogenetic Reconstructions Using nrDNA ITS Sequences - an Example from Potalieae (Gentianaceae: Asteridae)
inferred← citeshttps://doi.org/10.1600/036364415x686305openalex-snapshot
Is Sequence Alignment an Art or a Science?
inferred← citeshttps://doi.org/10.17760/d10019480openalex-snapshot
Bioinformatics applications through visualization of variations on protein structures, comparative functional genomics, and comparative modeling for protein structure studies
inferred← citeshttps://doi.org/10.17776/csj.842265openalex-snapshot
Multiple sequence alignment quality comparison in T-Coffee, MUSCLE and M-Coffee based on different benchmarks
inferred← citeshttps://doi.org/10.18130/v30n64openalex-snapshot
Characterization of the Transcription Factor and Transcriptionally Active Protein Gene Families in Cowpea (Vigna unguiculata L.)
inferred← citeshttps://doi.org/10.18174/12707openalex-snapshot
Graph-based methods for large-scale protein classification and orthology inference
inferred← citeshttps://doi.org/10.2197/ipsjtbio.1.2openalex-snapshot
Improvement in Speed and Accuracy of Multiple Sequence Alignment Program PRIME
inferred← citeshttps://doi.org/10.2197/ipsjtbio.2.74openalex-snapshot
Statistical Comparative Study of Multiple Sequence Alignment Scores of Iterative Refinement Algorithms
inferred← citeshttps://doi.org/10.2478/s11658-010-0010-8openalex-snapshot
Molecular systematics: A synthesis of the common methods and the state of knowledge
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.1457openalex-snapshot
Molecular phylogenetics of the North American snake tribe Thamnophiini
inferred← citeshttps://doi.org/10.3233/bme-151479openalex-snapshot
A comparative analysis of multiple sequence alignments for biological data
inferred← citeshttps://doi.org/10.32657/10356/73737openalex-snapshot
Molecular modeling and statistical analysis on proteins and lipids
inferred← citeshttps://doi.org/10.3390/a12120256openalex-snapshot
Parameterized Algorithms in Bioinformatics: An Overview
inferred← citeshttps://doi.org/10.3390/computation12020032openalex-snapshot
Accelerating Multiple Sequence Alignments Using Parallel Computing
inferred← citeshttps://doi.org/10.3390/computation3020177openalex-snapshot
A Guide to Phylogenetic Reconstruction Using Heterogeneous Models—A Case Study from the Root of the Placental Mammal Tree
inferred← citeshttps://doi.org/10.3390/electronics11162550openalex-snapshot
An Extended Instruction Set for Bioinformatics’ Multiple Sequence Alignment
inferred← citeshttps://doi.org/10.3390/genes13020170openalex-snapshot
Identification of HIV Rapid Mutations Using Differences in Nucleotide Distribution over Time
inferred← citeshttps://doi.org/10.3390/mps5020026openalex-snapshot
Genomic Fishing and Data Processing for Molecular Evolution Research
inferred← citeshttps://doi.org/10.35537/10915/119134openalex-snapshot
Análisis y registro de la biodiversidad de la producción hortícola platense de la provincia de Buenos Aires: Estudio del tomate ‘platense’
inferred← citeshttps://doi.org/10.36253/978-88-6655-045-7openalex-snapshot
Bioinformatics of genome evolution: from ancestral to modern metabolism
inferred← citeshttps://doi.org/10.4033/iee.2014.7.2.nopenalex-snapshot
Fishing for significance in phylogenies: too many alternatives for the same outcome, or an appeal to Journal editors
inferred← citeshttps://doi.org/10.4137/ebo.s18980openalex-snapshot
IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments
inferred← citeshttps://doi.org/10.48550/arxiv.1302.6030openalex-snapshot
A Fast Template Based Heuristic For Global Multiple Sequence Alignment
inferred← citeshttps://doi.org/10.48550/arxiv.1510.09037openalex-snapshot
Multiple sequence alignment for short sequences
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