M-Coffee statistics

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M-Coffee specifications

Information


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

Documentation


Maintainer


  • person_outline Cedric Notredame <>

Publication for M-Coffee

M-Coffee in publications

 (106)
PMCID: 5841299
PMID: 29515152
DOI: 10.1038/s41598-018-22540-1

[…] 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 […]

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

[…] at concentrations from 50 ng/μl to 100 ng/μl was 2 μl per well. the final volume of the qpcr reactions was 10 μl., 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 […]

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

[…] 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)., the two conformations/states, […]

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

[…] 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 […]

PMCID: 5795429
PMID: 29301233
DOI: 10.3390/v10010016

[…] (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 […]


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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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