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M-Coffee specifications


Unique identifier OMICS_14998
Name M-Coffee
Interface Web user interface
Restrictions to use None
Input data A set of sequences to align.
Input format FASTA
Programming languages C, Perl
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes



  • person_outline Cedric Notredame

Publication for M-Coffee

M-Coffee citations


Probing the Phylogenomics and Putative Pathogenicity Genes of Pythium insidiosum by Oomycete Genome Analyses

Sci Rep
PMCID: 5841299
PMID: 29515152
DOI: 10.1038/s41598-018-22540-1

[…] different software, which are MUSCLE v3.7, MAFFT v7.313 and Kalign v2.04 were used to create multiple sequence alignments in both forward and reverse directions (also known as Head or Tail approach). M-Coffee was then used to combine all six multiple sequence alignment results into a consensus alignment. Finally, trimAl v1.4rev22 was used to trim poorly aligned regions present in the consensus ali […]


Intrahost Norovirus Evolution in Chronic Infection Over 5 Years of Shedding in a Kidney Transplant Recipient

Front Microbiol
PMCID: 5840165
PMID: 29552005
DOI: 10.3389/fmicb.2018.00371

[…] The alignment of the haplotype deduced amino-acid sequences was performed using the M-Coffee software (http://tcoffee.crg.cat/apps/tcoffee/do:mcoffee; August 2017), with the default settings. The Jalview 2.10 software (Waterhouse et al., ) was used for visualization of the alignment […]


The End of a 60 year Riddle: Identification and Genomic Characterization of an Iridovirus, the Causative Agent of White Fat Cell Disease in Zooplankton

PMCID: 5873915
PMID: 29487186
DOI: 10.1534/g3.117.300429

[…] ntative sequences from the virus families Iridoviridae, Ascoviridae and Marseilleviridae (outgroup) downloaded from GenBank. The sequences were aligned using the meta-multiple sequence alignment tool M-Coffee (). Conserved blocks were determined with the program GBlocks version 0.91b, using parameter options that allowed for smaller final blocks, gap positions within the final blocks, and less str […]


A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia

Nat Commun
PMCID: 5802732
PMID: 29410408
DOI: 10.1038/s41467-017-02204-w

[…] on about genome size was taken from the web server http://www.bionumbers.hms.harvard.edu/default.aspx. Multiple sequence alignment of tRNAThr and tRNAThr(G4•U69) was prepared using T-Coffee server in M-Coffee mode (http://tcoffee.crg.cat/apps/tcoffee/do:mcoffee), while consensus sequence logo was prepared using WebLogo server (http://weblogo.berkeley.edu/logo.cgi). […]


Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo and autopolyploidization events

BMC Biol
PMCID: 5785856
PMID: 29370802
DOI: 10.1186/s12915-018-0482-y

[…] hen aligned using three different methods (MUSCLE v3.8, MAFFT v6.814b, and KALIGN 2.04) used in forward and reverse orientation [–]. A consensus alignment is reconstructed from these alignments using M-coffee []. This consensus alignment is then trimmed twice, first using a consistency score (0.1667) and then using a gap threshold (0.1) as implemented in trimAl v1.4 []. The resulting filtered alig […]


Analyses of Tissue Culture Adaptation of Human Herpesvirus 6A by Whole Genome Deep Sequencing Redefines the Reference Sequence and Identifies Virus Entry Complex Changes

PMCID: 5795429
PMID: 29301233
DOI: 10.3390/v10010016

[…] virus (EBV) strain B95-8 (PDB ID: 3fvc), and gB Herpes Simplex virus (HSV)-1, strain KOS (PDB ID: 2gum and 3nwa). Closest alignments were shown with HCMV gB, 45% identity, 65% similarity (meta method M-Coffee, see ). The models cover the ectodomain, residues 38–579, and domains I, II, III, and IV. The passage mutant, Thr193Ala, was modelled using swapaa command in Chimera []. The models of the HHV […]

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M-Coffee institution(s)
The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland; Laboratoire Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Marseille, France
M-Coffee funding source(s)
This work was supported by the CNRS (Centre National de la Recherche Scientifique), Sanofi-Aventis Pharma SA., Marseille-Nice Génopole and the French National Genomic Network (RNG). Part of this work is funded by the Science Foundation Ireland.

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