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The alignment of sets of sequences and the construction of phyletic trees: An integrated method
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/9780470122921.ch2openalex-snapshot
Prediction of the Secondary Structure of Proteins from their Amino Acid Sequence
inferredcites →https://doi.org/10.1007/bf01732010openalex-snapshot
Phylogenies from amino acid sequences aligned with gaps: The problem of gap weighting
inferredcites →https://doi.org/10.1007/bf01840887openalex-snapshot
Accuracy of estimated phylogenetic trees from molecular data
inferredcites →https://doi.org/10.1007/bf02100219openalex-snapshot
Computer comparison of new and existing criteria for constructing evolutionary trees from sequence data
inferredcites →https://doi.org/10.1007/bf02300753openalex-snapshot
Accuracy of estimated phylogenetic trees from molecular data
inferredcites →https://doi.org/10.1016/0001-8708(76)90202-4openalex-snapshot
Some biological sequence metrics
inferredcites →https://doi.org/10.1016/0010-4825(76)90027-5openalex-snapshot
Iterative character weighing in numerical taxonomy
inferredcites →https://doi.org/10.1016/0022-2836(70)90057-4openalex-snapshot
A general method applicable to the search for similarities in the amino acid sequence of two proteins
inferredcites →https://doi.org/10.1016/0022-2836(71)90390-1openalex-snapshot
Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c551
inferredcites →https://doi.org/10.1016/0022-5193(81)90233-2openalex-snapshot
A practical method for calculating evolutionary trees from sequence data
inferredcites →https://doi.org/10.1016/0022-5193(83)90343-0openalex-snapshot
Phenetic methods of classification use information that is disregarded by minimum-length methods
inferredcites →https://doi.org/10.1016/0031-3203(81)90054-6openalex-snapshot
Oligothetic characterisation of clusters
inferredcites →https://doi.org/10.1073/pnas.76.1.381openalex-snapshot
Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species.
inferredcites →https://doi.org/10.1073/pnas.76.9.4516openalex-snapshot
Calculation of evolutionary trees from sequence data.
inferredcites →https://doi.org/10.1093/nar/10.1.421openalex-snapshot
A strategy for sequence phylogeny research
inferredcites →https://doi.org/10.1093/nar/9.6.1451openalex-snapshot
Phylogenetic tree derived from bacterial, cytosol and organelle 5S rRNA sequences
inferredcites →https://doi.org/10.1126/science.202030openalex-snapshot
Origins of Prokaryotes, Eukaryotes, Mitochondria, and Chloroplasts
inferredcites →https://doi.org/10.1137/0126070openalex-snapshot
On the Theory and Computation of Evolutionary Distances
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria
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Seventy-five percent accuracy in protein secondary structure prediction
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Toward more meaningful hierarchical classification of protein three-dimensional structures
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Multiple Sequence Alignment Using ClustalW and ClustalX
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An Overview of Multiple Sequence Alignment
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CLUSTAL ( CLUSTALY , CLUSTALX )
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Phylogenetic Tree (Phylogenetic Reconstruction, Phylogeny, Phylogeny Reconstruction)
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Tree-Based Progressive Alignment
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The Basics of Protein Sequence Analysis
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Multiple Alignment
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Phylogenetic Tree (Phylogeny, Phylogeny Reconstruction, Phylogenetic Reconstruction)
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Tree‐based Progressive Alignment
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The yeast homologue of U3 snRNA.
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Structure‐Function analysis of human IL‐6: Identification of two distinct regions that are important for receptor binding
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A method to recognize distant repeats in protein sequences
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Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinement as Assessed by Reference to Structural Alignments
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Sequence profiles of immunoglobulin and immunoglobulin-like domains
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T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton
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HGA-COFFEE : Aligning Multiple Sequences by Hybrid Genetic Algorithm
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Using Secondary Structure Information to Perform Multiple Alignment
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On incremental computation of transitive closure and greedy alignment
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Phylogeny-Aware Alignment with PRANK and PAGAN
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Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation
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Comparative Structural and Functional Studies on Small Ribosomal RNAs
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Multiple Sequence Alignment
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Multiple Sequence Alignment
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Phylogeny-aware alignment with PRANK
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PRALINE: A Versatile Multiple Sequence Alignment Toolkit
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Heuristic Alignment Methods
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Tools and Methods in the Analysis of Simple Sequences
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Limitations in Computational Analysis of Retrovirus Evolution
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Multi-GPU Approach for Large-Scale Multiple Sequence Alignment
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Bioinformatics and Translation Initiation
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Protein Isoelectric Point and Helicobacter pylori
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A Survey of Multiple Sequence Alignment Techniques
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Towards Polyphony Reconstruction Using Multidimensional Multiple Sequence Alignment
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Melody Retrieval and Classification Using Biologically-Inspired Techniques
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Nucleotide Substitution Models and Evolutionary Distances
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Distance-Based Phylogenetic Methods
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Fundamentals of Proteomics
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A Method for Multiple Sequence Alignment Based on Particle Swarm Optimization
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Multiple Sequence Alignment Based on Chaotic PSO
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Multiple Sequence Alignment with Genetic Algorithms
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Alignment of Protein Sequences
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A Multigroup Parallel Genetic Algorithm for Multiple Sequence Alignment
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Molecular Systematics at the Species Boundary: Exploiting Conserved and Variable Regions of the Mitochondrial Genome of Animals via Direct Sequencing from Amplified DNA
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Wie funktionieren MSA-Programme?
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How Do MSA Programs Work?
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Multiple alignment of transmembrane protein sequences
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Similarity measures for structured data: a general framework and some applications to vegetation data
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Knowing When to Stop: Cluster Concept — Concept Cluster
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Hybrid Invasive Weed Optimization and GA for Multiple Sequence Alignment
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Multiple Sequence Alignment Algorithm Using Adaptive Evolutionary Clustering
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DNA Sequence Alignment and Phylogenetic Inferences: Guidelines for Analysis and the Selection of Appropriate Methods for Molecular Systematics
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Similarity measures for structured data: a general framework and some applications to vegetation data
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The 5S DNA units of bread wheat (Triticum aestivum)
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U1 snRNA: The evolution of its primary and secondary structure
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A multiple sequence comparison method
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Progressive sequence alignment as a prerequisitetto correct phylogenetic trees
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Piriformospora indica and Sebacina vermifera increase growth performance at the expense of herbivore resistance in Nicotiana attenuata
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A bi-objective function optimization approach for multiple sequence alignment using genetic algorithm
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Comparative Analysis and Molecular Evolution of Class I PI3K Regulatory Subunit p85α Reveal the Structural Similarity Between nSH2 and cSH2 Domains
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Partially Local Multi-way Alignments
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Homology modelling and 1H NMR studies of human leukaemia inhibitory factor
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Arguments against a close relationship between non‐phosphorylating and phosphorylating glyceraldehyde‐3‐phosphate dehydrogenases
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Pattern analysis of RNA secondary structure
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Definition of general topological equivalence in protein structures
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Anatomy and evolution of proteins displaying the viral capsid jellyroll topology
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Recognition of distantly related protein sequences using conserved motifs and neural networks
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The inference of evolutionary trees from molecular data
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A bibliography on computational molecular biology and genetics
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Phylogenetic inference based on matrix representation of trees
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Algorithms for Strings and Sequences: Multiple Alignment
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Algorithms for Strings and Sequences: Multiple Alignment
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Phylogenetic Analyses
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Pattern Recognition and Artificial Intelligence in Molecular Biology
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Using Genetic Algorithms for Pairwise and Multiple Sequence Alignments
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Multiobjective characteristic-based framework for very-large multiple sequence alignment
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Channelrhodopsins: A bioinformatics perspective
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Multiple sequence alignment with affine gap by using multi-objective genetic algorithm
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The PRALINE online server: optimising progressive multiple alignment on the web
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Caretta – A multiple protein structure alignment and feature extraction suite
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BCL::Align—Sequence alignment and fold recognition with a custom scoring function online
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Homology assessment and molecular sequence alignment
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3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments
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SARS-CoV-2 and other human coronaviruses: Mapping of protease recognition sites, antigenic variation of spike protein and their grouping through molecular phylogenetics
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Multiple sequence alignments
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Towards the accurate alignment of over a million protein sequences: Current state of the art
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Swarm intelligence for optimizing the parameters of multiple sequence aligners
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PhyPA: Phylogenetic method with pairwise sequence alignment outperforms likelihood methods in phylogenetics involving highly diverged sequences
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Weighting aligned protein or nucleic acid sequences to correct for unequal representation
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A survey of multiple sequence comparison methods
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Local weighting schemes for protein multiple sequence alignment
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Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment
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Weighted sequence graphs: boosting iterated dynamic programming using locally suboptimal solutions
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10 The Application of 16S rRNA Cataloguing and 5S rRNA Sequencing in Bacterial Systematics
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Chapter 4 Computational methods relating protein sequence and structure
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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
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Large multiple sequence alignments with a root-to-leaf regressive method
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Bacterial Foraging Optimization –Genetic Algorithm for Multiple Sequence Alignment with Multi-Objectives
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Multiple sequence alignment for phylogenetic purposes
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An algorithm for progressive multiple alignment of sequences with insertions
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Mind the gaps: Progress in progressive alignment
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Simple chained guide trees give high-quality protein multiple sequence alignments
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Rate constancy of globin gene evolution in placental mammals.
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Weighting in sequence space: a comparison of methods in terms of generalized sequences.
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Alignment and Topological Accuracy of the Direct Optimization approach via POY and Traditional Phylogenetics via ClustalW + PAUP*
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Harris Hawks Optimizer for Solving Multiple Sequence Alignment
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Multiple Sequence Alignment Based on a Suffix Tree and Center-Star Strategy: A Linear Method for Multiple Nucleotide Sequence Alignment on Spark Parallel Framework
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A survey on the algorithm and development of multiple sequence alignment
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MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
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Optimal alignment between groups of sequences and its application to multiple sequence alignment
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CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes
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Early bioinformatics: the birth of a discipline—a personal view
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SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures
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Upcoming challenges for multiple sequence alignment methods in the high-throughput era
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Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns
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Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees
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COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome
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Efficient merging of genome profile alignments
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Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit
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Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past
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Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes
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Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization
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Structure of aBacillus subtilisendo-β-l,4-glucanase gene
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Evolutionary origin, diversification and specialization of eukaryotic MutS homolog mismatch repair proteins
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
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M-Coffee: combining multiple sequence alignment methods with T-Coffee
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Refining multiple sequence alignments with conserved core regions
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PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences
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An nf-core framework for the systematic comparison of alternative modeling tools: the multiple sequence alignment case study
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Evolution of the primary and secondary structures of the E1a mRNAs of the adenovirus.
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ANTICALIgN: visualizing, editing and analyzing combined nucleotide and amino acid sequence alignments for combinatorial protein engineering
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Why Would Phylogeneticists Ignore Computerized Sequence Alignment?
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Multiple Sequence Alignment Methods. — Edited by David J. Russell.
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Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty
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A model of evolution and structure for multiple sequence alignment
inferred← citeshttps://doi.org/10.1099/0022-1317-65-10-1699openalex-snapshot
The Nucleotide Sequence of the Leftmost XhoI Fragment (6%) of Simian Adenovirus SA7P
inferred← citeshttps://doi.org/10.1101/077503openalex-snapshot
Co-estimation of Phylogeny-aware Alignment and Phylogenetic Tree
inferred← citeshttps://doi.org/10.1101/2021.12.20.473431openalex-snapshot
fastMSA: Accelerating Multiple Sequence Alignment with Dense Retrieval on Protein Language
inferred← citeshttps://doi.org/10.1101/490235openalex-snapshot
Fast and accurate large multiple sequence alignments using root-to-leave regressive computation
inferred← citeshttps://doi.org/10.1101/gr.076554.108openalex-snapshot
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
inferred← citeshttps://doi.org/10.1109/34.106998openalex-snapshot
Synthesis and recognition of sequences
inferred← citeshttps://doi.org/10.1109/bibe.2017.00-59openalex-snapshot
Multiple Sequence Alignment using Hybrid Parallel Computing
inferred← citeshttps://doi.org/10.1109/cec.2010.5586500openalex-snapshot
An evolutionary approach for performing multiple sequence alignment
inferred← citeshttps://doi.org/10.1109/csb.2004.120openalex-snapshot
MUSCLE: multiple sequence alignment with improved accuracy and speed
inferred← citeshttps://doi.org/10.1109/csb.2004.1332560openalex-snapshot
MUSCLE: multiple sequence alignment with improved accuracy and speed
inferred← citeshttps://doi.org/10.1109/eit.2008.4554299openalex-snapshot
A new heuristic for multiple sequence alignment
inferred← citeshttps://doi.org/10.1109/hicss.1992.183219openalex-snapshot
Minimum message length encoding, evolutionary trees and multiple-alignment
inferred← citeshttps://doi.org/10.1109/hpcsim.2013.6641425openalex-snapshot
Generating malware signature using transcoding from sequential data to amino acid sequence
inferred← citeshttps://doi.org/10.1109/icccas.2004.1346346openalex-snapshot
Aligning multiple sequences by genetic algorithm
inferred← citeshttps://doi.org/10.1109/iccitechn.2017.8281808openalex-snapshot
Cloud-POA: A cloud-based map only implementation of PO-MSA on Amazon multi-node EC2 Hadoop Cluster
inferred← citeshttps://doi.org/10.1109/ichi.2017.57openalex-snapshot
Evaluation of trace alignment quality and its application in medical process mining
inferred← citeshttps://doi.org/10.1109/icsess.2011.5982374openalex-snapshot
An improved algorithm for Multiple Sequence Alignment using Particle Swarm Optimization
inferred← citeshttps://doi.org/10.1109/ijsis.1996.565044openalex-snapshot
Fast and sound two-step algorithms for multiple alignment of nucleic sequences
inferred← citeshttps://doi.org/10.1109/itcc.2005.223openalex-snapshot
Parallel multiple sequence alignment with dynamic scheduling
inferred← citeshttps://doi.org/10.1109/sita.2016.7772273openalex-snapshot
Solving multiple RNA sequences alignment by multi-objective genetic algorithm method based on Pareto optimality
inferred← citeshttps://doi.org/10.1109/tcyb.2016.2621129openalex-snapshot
A Characteristic-Based Framework for Multiple Sequence Aligners
inferred← citeshttps://doi.org/10.1109/tevc.2015.2469546openalex-snapshot
A Hybrid Multiobjective Memetic Metaheuristic for Multiple Sequence Alignment
inferred← citeshttps://doi.org/10.1109/tkde.2006.197openalex-snapshot
Structured Data Extraction from the Web Based on Partial Tree Alignment
inferred← citeshttps://doi.org/10.1128/jb.00121-20openalex-snapshot
Molecular Design of a Signaling System Influences Noise in Protein Abundance under Acid Stress in Different Gammaproteobacteria
inferred← citeshttps://doi.org/10.1128/jb.00542-25openalex-snapshot
AdiY acts as a cytoplasmic pH sensor via histidine protonation to regulate acid stress adaptation in Escherichia coli
inferred← citeshttps://doi.org/10.1128/jvi.66.2.1139-1151.1992openalex-snapshot
Extensive sequence-specific information throughout the CAR/RRE, the target sequence of the human immunodeficiency virus type 1 Rev protein
inferred← citeshttps://doi.org/10.1128/jvi.66.2.632-640.1992openalex-snapshot
Novel GACG-hairpin pair motif in the 5' untranslated region of type C retroviruses related to murine leukemia virus
inferred← citeshttps://doi.org/10.1137/0152101openalex-snapshot
Multiple Alignment, Communication Cost, and Graph Matching
inferred← citeshttps://doi.org/10.1142/s0219720004000831openalex-snapshot
PROGRESSIVE MULTIPLE ALIGNMENT USING SEQUENCE TRIPLET OPTIMIZATIONS AND THREE-RESIDUE EXCHANGE COSTS
inferred← citeshttps://doi.org/10.1145/1060745.1060761openalex-snapshot
Web data extraction based on partial tree alignment
inferred← citeshttps://doi.org/10.1145/2811411.2811543openalex-snapshot
Extracting representative API patterns of malware families using multiple sequence alignments
inferred← citeshttps://doi.org/10.1145/3470850openalex-snapshot
Pedometer-free Geomagnetic Fingerprinting with Casual Walking Speed
inferred← citeshttps://doi.org/10.1145/3673038.3673094openalex-snapshot
Parallelization of the Banded Needleman & Wunsch Algorithm on UPMEM PiM Architecture for Long DNA Sequence Alignment
inferred← citeshttps://doi.org/10.1155/2014/974316openalex-snapshot
Computational Biophysical, Biochemical, and Evolutionary Signature of Human R-Spondin Family Proteins, the Member of Canonical Wnt/β-Catenin Signaling Pathway
inferred← citeshttps://doi.org/10.11606/d.45.2016.tde-20230727-113328openalex-snapshot
Alinhamento múltiplo de genomas e sequências de proteínas com repetições e rearranjos
inferred← citeshttps://doi.org/10.1177/0962280208099500openalex-snapshot
Stochastic models of sequence evolution including insertion—deletion events
inferred← citeshttps://doi.org/10.1186/1471-2105-11-570openalex-snapshot
Reticular alignment: A progressive corner-cutting method for multiple sequence 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/10.1186/1471-2105-5-113openalex-snapshot
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
inferred← citeshttps://doi.org/10.1186/1471-2105-8-254openalex-snapshot
Progressive multiple sequence alignments from triplets
inferred← citeshttps://doi.org/10.1186/1471-2105-9-137openalex-snapshot
How reliably can we predict the reliability of protein structure predictions?
inferred← citeshttps://doi.org/10.1186/1748-7188-5-21openalex-snapshot
Sequence embedding for fast construction of guide trees for multiple sequence alignment
inferred← citeshttps://doi.org/10.1186/s12859-015-0688-8openalex-snapshot
Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix
inferred← citeshttps://doi.org/10.1186/s12859-015-0696-8openalex-snapshot
MultiSETTER: web server for multiple RNA structure comparison
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