T-Coffee specifications

Information


Unique identifier OMICS_00989
Name Tree-based consistency objective function for alignment evaluation
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


Information


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

Documentation


T-Coffee articles

T-Coffee citations

 (21)
2018
PMCID: 5824068

[…] conserved among 11 geobacillus and 7 parageobacillus genomes, including the 3 genomes sequenced in this study. a total of 1,355 conserved proteins were identified using orthofinder 15, aligned using t-coffee 16, concatenated and trimmed using gblocks 17 before the resulting alignment (296,082 amino acids in length) was used to construct a core genome maximum likelihood phylogeny using phyml-sms […]

2016
PMCID: 4959661

[…] m. tuberculosis h37rv (caa49620.1), s. pneumoniae (ajd71681.1), e. coli f11 (edv68789.1), and k. pneumoniae (kla37751.1). alignment of the full sequences of all six strains was conducted with the t-coffee multiple-sequence alignment software (see text s1) (http://tcoffee.crg.cat/apps/tcoffee/do:regular) and formatted with the boxshade program (http://www.ch.embnet.org/software/box_form.html) […]

2016
PMCID: 4853749

[…] al., 2006). all blastn analyses against bud s10's genome were performed with a cutoff e-value of 10e−5., arsenite oxidoreductase (aioa) peptide sequences were aligned with the expresso algorithm in t-coffee using default parameters (armougom et al., 2006), and the alignment trimmed with the “automated1” option in trimal (capella-gutiérrez et al., 2009) at the phylomon2 online workbench (sánchez […]

2016
PMCID: 4787006

[…] genes, in particular for a 6-gene family and for their orthologs in other insect species. a phylogenetic study of this gene family was performed: the proteic alignment was obtained with t-coffee [29] then trimmed with gblocks [30]. the phylogeny was obtained using mega6 [31], using a ml method and evaluating bootstrap support for nodes (1000 replicates)., normalization of read […]

2015
PMCID: 4683645

[…] gene was standardized using the included scaling function in pheatmap., the pth11 protein sequence from magnaporthe oryzae and the 25 pth11-related n. crassa gpcr protein sequences were aligned with t-coffee using default parameters and trimmed using trimal with a threshold of 0.7 (notredame et al. 2000; capella-gutierrez et al. 2009). the programs seqboot, protpars, and consense, belonging […]

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

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