(Q38651602)

5 September 2017

title

Multiple sequence alignment modeling: methods and applications (English)

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5 September 2017

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5 September 2017

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5 September 2017

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Cedric Notredame

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Carsten Kemena

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Carsten Kemena

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Giovanni Bussotti

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Giovanni Bussotti

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author name string

Maria Chatzou

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5 September 2017

Cedrik Magis

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5 September 2017

language of work or name

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27 November 2015

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Briefings in Bioinformatics

5 September 2017

published in

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5 September 2017

volume

17

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5 September 2017

issue

6

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5 September 2017

page(s)

1009-1023

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https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

5 September 2017

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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Multiple sequence alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

SAGA: sequence alignment by genetic algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

The alignment of sets of sequences and the construction of phyletic trees: an integrated method

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

A general method applicable to the search for similarities in the amino acid sequence of two proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

T-Coffee: A novel method for fast and accurate multiple sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

ProbCons: Probabilistic consistency-based multiple sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Evaluation of iterative alignment algorithms for multiple alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Multiple alignment by aligning alignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

DIALIGN: finding local similarities by multiple sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Segment-based multiple sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Epistasis as the primary factor in molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Sequence embedding for fast construction of guide trees for multiple sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

An algorithm for progressive multiple alignment of sequences with insertions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Class of multiple sequence alignment algorithm affects genomic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Twilight zone of protein sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Protein secondary structure prediction based on position-specific scoring matrices

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

PROMALS3D: a tool for multiple protein sequence and structure alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

3DCoffee: combining protein sequences and structures within multiple sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Predicting a set of minimal free energy RNA secondary structures common to two sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Accelerated probabilistic inference of RNA structure evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Finding the most significant common sequence and structure motifs in a set of RNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

A fast structural multiple alignment method for long RNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

The equilibrium partition function and base pair binding probabilities for RNA secondary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Murlet: a practical multiple alignment tool for structural RNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Alignment of RNA base pairing probability matrices

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Multiple structural alignment and clustering of RNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

LocARNA-P: accurate boundary prediction and improved detection of structural RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

CARNA--alignment of RNA structure ensembles

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

A max-margin model for efficient simultaneous alignment and folding of RNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

R-Coffee: a method for multiple alignment of non-coding RNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Local RNA base pairing probabilities in large sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

RNA structure alignment by a unit-vector approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

SARSA: a web tool for structural alignment of RNA using a structural alphabet

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

RALEE--RNA ALignment editor in Emacs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Semiautomated improvement of RNA alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

BlastR--fast and accurate database searches for non-coding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Long noncoding RNAs with enhancer-like function in human cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Nucleosome positioning as a determinant of exon recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Multiple genome rearrangement and breakpoint phylogeny.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Aligning multiple whole genomes with Mercator and MAVID.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Mugsy: fast multiple alignment of closely related whole genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Aligning multiple genomic sequences with the threaded blockset aligner

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

A novel method for multiple alignment of sequences with repeated and shuffled elements

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Cactus: Algorithms for genome multiple sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Genome alignment with graph data structures: a comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Alignathon: a competitive assessment of whole-genome alignment methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

PSAR: measuring multiple sequence alignment reliability by probabilistic sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Assessing computational methods of cis-regulatory module prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Computational strategies for the genome-wide identification of cis-regulatory elements and transcriptional targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Use of ChIP-Seq data for the design of a multiple promoter-alignment method

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

COFFEE: an objective function for multiple sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Quality measures for protein alignment benchmarks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Making automated multiple alignments of very large numbers of protein sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

ProSup: a refined tool for protein structure alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

The iRMSD: a local measure of sequence alignment accuracy using structural information

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

A benchmark of multiple sequence alignment programs upon structural RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Rose: generating sequence families.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

INDELible: a flexible simulator of biological sequence evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Multiple sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Multiple sequence alignment accuracy and evolutionary distance estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

The impact of multiple protein sequence alignment on phylogenetic estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

STRIKE: evaluation of protein MSAs using a single 3D structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

AL2CO: calculation of positional conservation in a protein sequence alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

An alignment confidence score capturing robustness to guide tree uncertainty

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

RASCAL: rapid scanning and correction of multiple sequence alignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Quantifying the local reliability of a sequence alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

A polyhedral approach to sequence alignment problems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

Multiple Sequence Alignment Accuracy and Phylogenetic Inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV099

21 January 2018

Identifiers

DOI

10.1093/BIB/BBV099

1 reference

journals/bib/ChatzouMCKBEN16

5 September 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference