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TCS specifications

Information


Unique identifier OMICS_08067
Name TCS
Alternative name Transitive Consistency Score
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Cédric Notredame <>

Information


Unique identifier OMICS_08067
Name TCS
Alternative name Transitive Consistency Score
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Cédric Notredame <>

Publications for Transitive Consistency Score

TCS in publications

 (9)
PMCID: 5760710
PMID: 29317655
DOI: 10.1038/s41467-017-02680-0

[…] enzymes are homologs of mphs, and therefore aph(2”)-iia, aph(2”)-iiia, and aph(2′′)-ie were used as outgroups for rooting the tree. the alignment was then weighted by alignment confidence using the transitive consistency score (tcs) function of t-coffee. raxml was used to generate a maximum likelihood phylogenetic tree with the gamma model of rate heterogeneity and lg empirical base frequencies […]

PMCID: 5758724
PMID: 29311627
DOI: 10.1038/s41598-017-18115-1

[…] proteins and ribosomal proteins were aligned using fast statistical alignment (fsa) (v1.1.5.9). phylogenetically informative positions were determined from the alignments and extracted using the transitive consistency score (tcs) implementation within t-coffee (v11.00.d27cadf) and concatenated trees had individual protein alignments concatenated using seaview. phylogenetic inference was made […]

PMCID: 5404901
PMID: 28469382
DOI: 10.1177/1176934317703401

[…] using hmm profiles, multiple alignments were conducted for amino acid sequences from each cazy gh family, using the clustal omega algorithm. the quality of gh alignments was evaluated using the transitive consistency score (tcs) statistics available in t-coffee platform. as tcs assigns a score for each site in an alignment, it allows verification of the overall alignment’s quality. […]

PMCID: 5397798
PMID: 28435440
DOI: 10.1186/s13015-017-0102-3

[…] which is in turn dominated by zorro. (guidance also requires four or more sequences, which excludes many benchmarks.) below we briefly summarize the approaches behind tcs and zorro., tcs (short for “transitive consistency score”) extends an earlier approach of coffee []. for a pair i, j of residues that are aligned in a column and that come from sequences a and b, the support for aligned pair i,  […]

PMCID: 5483954
PMID: 28126723
DOI: 10.1042/BSR20160529

[…] no: cag33272.1] (class 2) were identified using protein blast search. multiple sequences of the above mentioned aldhs along with ald4p and ald6p sequences from the present study were aligned using transitive consistency score (tcs) web server available from http://tcoffee.crg.cat/tcs to determine their homology and conservation of domain residues []. the sequence homology was evaluated using […]


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TCS institution(s)
Comparative Bioinformatics, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
TCS funding source(s)
Plan Nacional [BFU2011–28575 to C.N. and P.D.]; Center for Genomics Regulation (CRG); ‘Fundació Obra Social la Caixa’ (to J.-M.C.); European Research Council [ERC-2008-AdG No 232947 to J.-M.C.]; RENABI IFB (to O.G. and V.L.); Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017’, SEV-2012–0208. Computational resources are provided by the Center for Genomic Regulation (CRG)

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