PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

[BibT_eX]

[DOI]

Evan W. Floden

Paolo Di Tommaso

Nucleic Acids Res., 2016

Multiple sequence alignment modeling: methods and applications.

[BibT_eX]

[DOI]

Briefings Bioinform., 2016

2015

Recovering accuracy methods for scalable consistency library.

[BibT_eX]

[DOI]

J. Supercomput., 2015

High Performance computing improvements on bioinformatics consistency-based multiple sequence alignment tools.

[BibT_eX]

[DOI]

Parallel Comput., 2015

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2015

2014

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2014

2013

Improving multiple sequence alignment biological accuracy through genetic algorithms.

[BibT_eX]

[DOI]

J. Supercomput., 2013

Performance analysis of computational approaches to solve Multiple Sequence Alignment.

[BibT_eX]

[DOI]

J. Supercomput., 2013

T-RMSD: a web server for automated fine-grained protein structural classification.

[BibT_eX]

[DOI]

Cedrik Magis

Paolo Di Tommaso

Cédric Notredame

Nucleic Acids Res., 2013

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

[BibT_eX]

[DOI]

Bioinform., 2013

Scalability and accuracy improvements of consistency-based multiple sequence alignment tools.

[BibT_eX]

[DOI]

Proceedings of the 20th European MPI Users's Group Meeting, 2013

2012

Epistasis as the primary factor in molecular evolution.

[BibT_eX]

[DOI]

Nat., 2012

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

AMPA: an automated web server for prediction of protein antimicrobial regions.

[BibT_eX]

[DOI]

Bioinform., 2012

Enhancing the Scalability of Consistency-based Progressive Multiple Sequences Alignment Applications.

[BibT_eX]

[DOI]

Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium, 2012

2011

Exploiting parallelism on progressive alignment methods.

[BibT_eX]

[DOI]

J. Supercomput., 2011

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2011

A user-friendly web portal for T-Coffee on supercomputers.

[BibT_eX]

[DOI]

BMC Bioinform., 2011

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

[BibT_eX]

[DOI]

Bioinform., 2011

2010

Predicting phenotypic traits of prokaryotes from protein domain frequencies.

[BibT_eX]

[DOI]

BMC Bioinform., 2010

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

[BibT_eX]

[DOI]

Bioinform., 2010

2009

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

[BibT_eX]

[DOI]

Carsten Kemena

Cédric Notredame

Bioinform., 2009

2008

R-Coffee: a web server for accurately aligning noncoding RNA sequences.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2008

Segment-based multiple sequence alignment.

[BibT_eX]

[DOI]

Proceedings of the ECCB'08 Proceedings, 2008

2007

Recent Evolutions of Multiple Sequence Alignment Algorithms.

[BibT_eX]

[DOI]

Cédric Notredame

PLoS Comput. Biol., 2007

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2007

2006

PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2006

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

[BibT_eX]

[DOI]

Nucleic Acids Res., 2006

APDB: a web server to evaluate the accuracy of sequence alignments using structural information.

[BibT_eX]

[DOI]

Bioinform., 2006

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

[BibT_eX]

[DOI]

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

Invited Talk: Combining Sequence Information with T-Coffee.

[BibT_eX]

[DOI]

Cédric Notredame

Proceedings of the German Conference on Bioinformatics GCB 2006, 19.09. 2006, 2006

2004

3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2004

CaspR: a web server for automated molecular replacement using homology modelling.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2004

2003

Tcoffee add igs: a web server for computing, evaluating and combining multiple sequence alignments.

[BibT_eX]

[DOI]

Olivier Poirot

Eamonn O'Toole

Cédric Notredame

Nucleic Acids Res., 2003

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

[BibT_eX]

[DOI]

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2001

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2001

Mocca: semi-automatic method for domain hunting.

[BibT_eX]

[DOI]

Cédric Notredame

Bioinform., 2001

1998

Optimization of ribosomal RNA profile alignments.

[BibT_eX]

[DOI]

Emmet A. O'Brien

Cédric Notredame

Desmond G. Higgins

Bioinform., 1998

COFFEE: an objective function for multiple sequence alignments.

[BibT_eX]

[DOI]

Cédric Notredame

Liisa Holm

Desmond G. Higgins

Bioinform., 1998

Cédric Notredame

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