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T-Coffee specifications

Information


Unique identifier OMICS_00989
Name T-Coffee
Alternative names Tree-based consistency objective function for alignment evaluation, tcoffee
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Additional information


http://tcoffee.crg.cat/apps/tcoffee/do:regular

Information


Unique identifier OMICS_00989
Name T-Coffee
Alternative names Tree-based consistency objective function for alignment evaluation, tcoffee
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Additional information


http://tcoffee.crg.cat/apps/tcoffee/do:regular

Publications for Tree-based consistency objective function for alignment evaluation

T-Coffee citations

 (1034)
library_books

Selective dissociation between LSD1 and GFI1B by a LSD1 inhibitor NCD38 induces the activation of ERG super enhancer in erythroleukemia cells

2018
Oncotarget
PMCID: 5940392
PMID: 29765516
DOI: 10.18632/oncotarget.24774

[…] sing ECR browser (http://ecrbrowser.dcode.org/). Genomic sequence spanning the ERG locus was obtained from UCSC genome browser (https://genome.ucsc.edu/). DNA sequence alignments were performed using T-coffee server (http://tcoffee.vital-it.ch/apps/tcoffee/do:regular). TF binding sites were analyzed with R-VISTA (http://rvista.dcode.org/). […]

library_books

Comparative Genomics Reveals Thousands of Novel Chemosensory Genes and Massive Changes in Chemoreceptor Repertories across Chelicerates

2018
Genome Biol Evol
PMCID: 5952958
DOI: 10.1093/gbe/evy081

[…] topology for the 11 species. For the analysis, we used OrthoMCL (v2.0.9; ) to identify 1:1 orthologs by clustering the sequences by similarity and then generated an MSA (for each ortholog group) with T-Coffee v11.00 (mcoffe mode; ). After filtering the MSAs with trimAl v1.4 (-automated1 option; ), we estimated the best-fit amino acid substitution model for each MSA with the program jModelTest base […]

library_books

Unifying the global phylogeny and environmental distribution of ammonia oxidising archaea based on amoA genes

2018
Nat Commun
PMCID: 5904100
PMID: 29666365
DOI: 10.1038/s41467-018-03861-1

[…] similarity and different length among proteins, sequences of each subunit were separately aligned with 14 different methods: L-INS-i, E-INS-i and G-INS-i strategies of MAFFT v7; PSI-Coffee, EXPRESSO; T-Coffee; ProbCons v1.12; Probalign v1.3; Prank; Muscle v3.7; MSAProbs v0.9.7; Kalign; Dialign-TX; and Clustal Omega. The 10 best alignments were selected after evaluation with MUMSA based on multiple […]

call_split

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

2018
PLoS Comput Biol
PMCID: 5919687
PMID: 29659563
DOI: 10.1371/journal.pcbi.1006101
call_split See protocol

[…] To allow a unified mapping of aaRS binding sites, an MSA of 81 (75) representative wild type sequences of Class I (Class II) ( and Files) aaRS was performed. The alignment was calculated with the T-Coffee expresso pipeline [], which guides the alignment by structural information. Using the obtained MSA ( and Files), residues in all aaRS structures were renumbered with the custom script “MSA P […]

call_split

The γ33 subunit of R phycoerythrin from Gracilaria chilensis has a typical double linked phycourobilin similar to γ subunit

2018
PLoS One
PMCID: 5892909
PMID: 29634783
DOI: 10.1371/journal.pone.0195656
call_split See protocol

[…] nucleotide sequences of the γ subunits genes were translated in silico by ExPASy Translate (http://expasy.org). Putative chromophorylation sites were found through a multiple sequence alignment using T-Coffee [] of γ33 subunits from red algae and experimentally determined chromophorylation sites from Gastroclonium coulteri [] and Griffithsia pacifica []. Secondary structure features were calculate […]

call_split

Deletion of a Gene Encoding a Putative Peptidoglycan Associated Lipoprotein Prevents Degradation of the Crystalline Region of Cellulose in Cytophaga hutchinsonii

2018
Front Microbiol
PMCID: 5891637
PMID: 29666619
DOI: 10.3389/fmicb.2018.00632
call_split See protocol

[…] The genome sequence of C. hutchinsonii was obtained from the NCBI database. CLUSTALW was used for the multiple alignment of related Pals. T-COFFEE and MUSCLE were applied to verify the CLUSTALW results. BoxShade was a tool to shade multiple alignment files. […]

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T-Coffee institution(s)
Centre For Genomic Regulation (Pompeu Fabra University), Barcelona, Spain

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