T-Coffee (Tree-based Consistency Objective Function For alignment Evaluation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from PDB files (3D-Coffee).

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  • T-Coffee (Tree-based Consistency Objective Function For alignment Evaluation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from PDB files (3D-Coffee). It has advanced features to evaluate the quality of the alignments and some capacity for identifying occurrence of motifs (Mocca). It produces alignment in the aln format by default, but can also produce PIR, MSF and FASTA format. The most common input formats are supported. While the default output is a Clustal-like format, it is sufficiently different from the output of ClustalW/X that many programs supporting Clustal format cannot read it; fortunately ClustalX can import T-Coffee output so the simplest fix for this issue is usually to import T-Coffee's output into ClustalX and then re-export. Another possibility is to request the strict Clustalw output format with the option "-output=clustalw_aln" An important specificity of T-Coffee is its ability to combine different methods and different data types. In its latest version, T-Coffee can be used to combine protein sequences and structures, RNA sequences and structures. It can also run and combine the output of the most common sequence and structure alignment packages. For a complete list see: tclinkdb. txt T-Coffee comes along with a sophisticated sequence reformatting utility named seq_reformat. An extensive documentation is available from t_coffee_technical. htm along with a tutorial t_coffee_tutorial. htm
  • T-Coffee (del inglés Tree-based Consistency Objective Function For alignment Evaluation, función objetivo de coherencia basada en árbol para evaluación de alineamientos) es un software para el alineamiento múltiple de secuencias que utiliza un enfoque progresivo. Genera una biblioteca de alineamientos de pares para guiar el alineamiento múltiple de secuencias. Puede combinar, también, alineamientos múltiples obtenidos previamente y, en las últimas versiones, puede usar información estructural de archivos PDB (3D-Coffee). Tiene características avanzadas para evaluar la calidad de los alineamientos, así como algunas capacidades para identificar la ocurrencia de motivos (Mocca). Por defecto, el alineamiento lo produce en el formato "aln" de Clustal, aunque también puede generar formatos PIR, MSF y FASTA. Los ficheros de entrada siempre están bajo el formato FASTA. Nótese que lo que T-Coffee denomina formato "Clustal" es lo bastante diferente del formato de salida de ClustalW/X como para que muchos programas que soportan el formato de Clustal no puedan leerlo; afortunadamente, ClustalX puede importar salidas de T-Coffee, por lo que un sencilla solución para este punto en cuestión es importar la salida de T-Coffee en ClustalX y re-exportarla.
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  • Cédric Notredame, CRG Centro de Regulacio Genomica - Barcelona
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  • Bioinformatics tool
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  • 8.06 (xsd:double)
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dbpprop:name
  • T-Coffee
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  • T-Coffee (Tree-based Consistency Objective Function For alignment Evaluation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from PDB files (3D-Coffee).
  • T-Coffee (del inglés Tree-based Consistency Objective Function For alignment Evaluation, función objetivo de coherencia basada en árbol para evaluación de alineamientos) es un software para el alineamiento múltiple de secuencias que utiliza un enfoque progresivo. Genera una biblioteca de alineamientos de pares para guiar el alineamiento múltiple de secuencias.
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  • T-Coffee
  • T-Coffee
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  • T-Coffee
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